BLASTP 2.2.26 [Sep-21-2011]


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= psy15215
         (1432 letters)

Database: nr 
           23,463,169 sequences; 8,064,228,071 total letters

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



>gi|134093713|ref|YP_001098788.1| sigma 70 factor of RNA polymerase [Herminiimonas arsenicoxydans]
          Length = 858

 Score =  933 bits (2412), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 462/637 (72%), Positives = 533/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE II 
Sbjct: 222  KDAFSNDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIG 280

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 281  TFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 340

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDEIV
Sbjct: 341  REMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIV 400

Query: 987  DGLIDKNFS--------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL+D N S                    +  +   EE+    S +A  S+EQLE+LK +
Sbjct: 401  DGLVDMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQLEQLKRD 460

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 461  SLAKFSTIAMQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQ 520

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V QIEKQIL+I VN+C MPR HFIKVFP NE NL+WVD E +  H Y+++L RN+P+
Sbjct: 521  VDEVRQIEKQILDIAVNRCEMPRNHFIKVFPGNETNLDWVDGEVEGNHPYSIVLARNVPA 580

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            +KELQQKLI+LQ  +VLPL DLR INRKM AGEMKARKAKREMTEANLRLVISIAKKYT+
Sbjct: 581  VKELQQKLIDLQARVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKYTN 640

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 641  RGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHM 700

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 701  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 760

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 761  SHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 820

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 821  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 857



 Score =  915 bits (2364), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 453/625 (72%), Positives = 524/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE I
Sbjct: 220 LLKDAFSNDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGI 278

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 279 IGTFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRM 338

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDE
Sbjct: 339 YMREMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDE 398

Query: 195 IVDGLIDKNFS--------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLK 240
           IVDGL+D N S                    +  +   EE+    S +A  S+EQLE+LK
Sbjct: 399 IVDGLVDMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQLEQLK 458

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            +SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 459 RDSLAKFSTIAMQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLR 518

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V QIEKQIL+I VN+C MPR HFIKVFP NE NL+WVD E +  H Y+++L RN+
Sbjct: 519 GQVDEVRQIEKQILDIAVNRCEMPRNHFIKVFPGNETNLDWVDGEVEGNHPYSIVLARNV 578

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P++KELQQKLI+LQ  +VLPL DLR INRKM AGEMKARKAKREMTEANLRLVISIAKKY
Sbjct: 579 PAVKELQQKLIDLQARVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKY 638

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 639 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPV 698

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 699 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 758

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 759 DDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 818

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 819 EVGKQFDVTRERIRQIEAKALRKLR 843


>gi|193222233|emb|CAL60659.2| putative RNA polymerase sigma factor rpoD (Sigma-70) [Herminiimonas
            arsenicoxydans]
          Length = 800

 Score =  932 bits (2409), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 462/637 (72%), Positives = 533/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE II 
Sbjct: 164  KDAFSNDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIG 222

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 223  TFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 282

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDEIV
Sbjct: 283  REMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDEIV 342

Query: 987  DGLIDKNFS--------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL+D N S                    +  +   EE+    S +A  S+EQLE+LK +
Sbjct: 343  DGLVDMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQLEQLKRD 402

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 403  SLAKFSTIAMQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQ 462

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V QIEKQIL+I VN+C MPR HFIKVFP NE NL+WVD E +  H Y+++L RN+P+
Sbjct: 463  VDEVRQIEKQILDIAVNRCEMPRNHFIKVFPGNETNLDWVDGEVEGNHPYSIVLARNVPA 522

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            +KELQQKLI+LQ  +VLPL DLR INRKM AGEMKARKAKREMTEANLRLVISIAKKYT+
Sbjct: 523  VKELQQKLIDLQARVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKYTN 582

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 583  RGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHM 642

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 643  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 702

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 703  SHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 762

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 763  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 799



 Score =  914 bits (2361), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 453/625 (72%), Positives = 524/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE I
Sbjct: 162 LLKDAFSNDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGI 220

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 221 IGTFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRM 280

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDE
Sbjct: 281 YMREMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIMAAAERISKDEAKIDE 340

Query: 195 IVDGLIDKNFS--------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLK 240
           IVDGL+D N S                    +  +   EE+    S +A  S+EQLE+LK
Sbjct: 341 IVDGLVDMNASEPVIAPPAPAAASDEEEEEEEEEEAEEEEETPAASGAAGFSSEQLEQLK 400

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            +SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 401 RDSLAKFSTIAMQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLR 460

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V QIEKQIL+I VN+C MPR HFIKVFP NE NL+WVD E +  H Y+++L RN+
Sbjct: 461 GQVDEVRQIEKQILDIAVNRCEMPRNHFIKVFPGNETNLDWVDGEVEGNHPYSIVLARNV 520

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P++KELQQKLI+LQ  +VLPL DLR INRKM AGEMKARKAKREMTEANLRLVISIAKKY
Sbjct: 521 PAVKELQQKLIDLQARVVLPLPDLRAINRKMAAGEMKARKAKREMTEANLRLVISIAKKY 580

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 581 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPV 640

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 641 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 700

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 701 DDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 760

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 761 EVGKQFDVTRERIRQIEAKALRKLR 785


>gi|300310204|ref|YP_003774296.1| RNA polymerase sigma-70 factor transcription regulator protein
            [Herbaspirillum seropedicae SmR1]
 gi|300072989|gb|ADJ62388.1| RNA polymerase sigma-70 factor transcription regulator protein
            [Herbaspirillum seropedicae SmR1]
          Length = 850

 Score =  927 bits (2396), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 465/637 (72%), Positives = 529/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE II 
Sbjct: 214  KDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIG 272

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 273  TFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 332

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AA++ISK+EIK+DEIV
Sbjct: 333  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAAERISKDEIKVDEIV 392

Query: 987  DGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL+D N S                    +      EE     S +A  S EQLE+LK +
Sbjct: 393  DGLVDPNESEQQVEAASSDSDEDDEDEEEEEEDEEEEESESTGSGAAGFSAEQLEQLKRD 452

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            +L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 453  ALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQ 512

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+P+
Sbjct: 513  VDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNVPA 572

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKYT+
Sbjct: 573  IKELQQKLIDLQARVVLPLQDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTN 632

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 633  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 692

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 693  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 752

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 753  SHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEV 812

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 813  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 849



 Score =  908 bits (2347), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 456/625 (72%), Positives = 520/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE I
Sbjct: 212 LLKDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGI 270

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 271 IGTFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 330

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AA++ISK+EIK+DE
Sbjct: 331 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAAERISKDEIKVDE 390

Query: 195 IVDGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 240
           IVDGL+D N S                    +      EE     S +A  S EQLE+LK
Sbjct: 391 IVDGLVDPNESEQQVEAASSDSDEDDEDEEEEEEDEEEEESESTGSGAAGFSAEQLEQLK 450

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            ++L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 451 RDALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLR 510

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+
Sbjct: 511 AQVDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNV 570

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P+IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 571 PAIKELQQKLIDLQARVVLPLQDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKY 630

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 631 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 690

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 691 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 750

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 751 DDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 810

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 811 EVGKQFDVTRERIRQIEAKALRKLR 835


>gi|398836332|ref|ZP_10593669.1| RNA polymerase sigma factor, sigma-70 family [Herbaspirillum sp.
            YR522]
 gi|398211966|gb|EJM98577.1| RNA polymerase sigma factor, sigma-70 family [Herbaspirillum sp.
            YR522]
          Length = 845

 Score =  926 bits (2394), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 465/637 (72%), Positives = 531/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIKLGKERG+LT+SEIND LPE+I+D E IE II 
Sbjct: 209  KDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTYSEINDHLPENIVDPEAIEGIIG 267

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M IS+ EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 268  TFADMGISLYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 327

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DEIV
Sbjct: 328  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDEIV 387

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIE--------------SSSADLSTEQLEKLKYE 1032
            DGL+D N S          ++ E++   E              + +A  S EQLE+LK +
Sbjct: 388  DGLVDLNESVQQVEAASASDDEEDEEDDEDEEDEEEESEGTGTAGAAGFSAEQLEQLKRD 447

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            +L KF  I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 448  ALGKFGVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRAQ 507

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V Q+E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+++L RN+P+
Sbjct: 508  VEEVRQVERQILDVAVNKCNMPRNHFIKVFPGNEVNLDWVDGEVAGNHDYSVVLARNVPA 567

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IKELQQKLI+LQ  +VLPL DLR INRKM AGE KAR AKREMTEANLRLVISIAKKYT+
Sbjct: 568  IKELQQKLIDLQARVVLPLPDLRAINRKMGAGEKKARMAKREMTEANLRLVISIAKKYTN 627

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 628  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 687

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 688  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 747

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 748  SHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEV 807

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 808  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 844



 Score =  908 bits (2346), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 456/625 (72%), Positives = 522/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIKLGKERG+LT+SEIND LPE+I+D E IE I
Sbjct: 207 LLKDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTYSEINDHLPENIVDPEAIEGI 265

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M IS+ EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 266 IGTFADMGISLYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 325

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DE
Sbjct: 326 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDE 385

Query: 195 IVDGLIDKNFSSNNRVIKGNKNNNEEKILIE--------------SSSADLSTEQLEKLK 240
           IVDGL+D N S          ++ E++   E              + +A  S EQLE+LK
Sbjct: 386 IVDGLVDLNESVQQVEAASASDDEEDEEDDEDEEDEEEESEGTGTAGAAGFSAEQLEQLK 445

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            ++L KF  I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 446 RDALGKFGVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLR 505

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+ +V Q+E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+++L RN+
Sbjct: 506 AQVEEVRQVERQILDVAVNKCNMPRNHFIKVFPGNEVNLDWVDGEVAGNHDYSVVLARNV 565

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P+IKELQQKLI+LQ  +VLPL DLR INRKM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 566 PAIKELQQKLIDLQARVVLPLPDLRAINRKMGAGEKKARMAKREMTEANLRLVISIAKKY 625

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 626 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 685

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 686 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 745

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 746 DDSHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 805

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 806 EVGKQFDVTRERIRQIEAKALRKLR 830


>gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma factor [Janthinobacterium sp. Marseille]
 gi|151280838|gb|ABR89248.1| RNA polymerase primary sigma factor [Janthinobacterium sp. Marseille]
          Length = 826

 Score =  926 bits (2392), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 455/638 (71%), Positives = 532/638 (83%), Gaps = 20/638 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE II 
Sbjct: 189  KDAFSSDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGIIG 247

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 248  TFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 307

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDEIV
Sbjct: 308  REMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIIAAAERISKDEAKIDEIV 367

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEK---------------ILIESSSADLSTEQLEKLKY 1031
            DGL+D + +           +++++                   S +A  S+EQLE+LK 
Sbjct: 368  DGLVDMDAAEPVVAPPAPAASSDDEEDEEEEEEEEEEEEETTAASGAAGFSSEQLEQLKR 427

Query: 1032 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 1091
            +SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+L IRFTAK +EKLCDTLR 
Sbjct: 428  DSLAKFSTIAQQFDKMRKAFEKEGYNSKPYVKAQEIISNELLSIRFTAKVVEKLCDTLRG 487

Query: 1092 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 1151
            Q+++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL+WVD E   +H Y+++L RN+P
Sbjct: 488  QVDEVRHIEKQILDVAVNRCGMPRGHFIKVFPGNETNLDWVDGEVNGKHAYSVVLARNVP 547

Query: 1152 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
            ++KELQQKLI+LQ  +VLPL DLR IN+KM AGEMKARKAKREMTEANLRLVISIAKKYT
Sbjct: 548  TVKELQQKLIDLQARVVLPLPDLRAINKKMAAGEMKARKAKREMTEANLRLVISIAKKYT 607

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 608  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVH 667

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 668  MIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDD 727

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 728  DSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEE 787

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 788  VGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 825



 Score =  907 bits (2344), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 448/626 (71%), Positives = 523/626 (83%), Gaps = 20/626 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+IID E IE I
Sbjct: 187 LLKDAFSSDTEA-SEEELEARRQKLKTLIKFGKERGFLTYAEINDHLPENIIDPEAIEGI 245

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V E   D ETL+LS+    + SDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 246 IGTFNDMGIAVYEQAPDAETLLLSDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRM 305

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEI+IAKRIE+GL+DMI AIS+CPTTI EI+ AA++ISK+E KIDE
Sbjct: 306 YMREMGSVELLTREGEIDIAKRIEDGLRDMIQAISACPTTIAEIIAAAERISKDEAKIDE 365

Query: 195 IVDGLIDKNFSSNNRVIKGNKNNN---------------EEKILIESSSADLSTEQLEKL 239
           IVDGL+D + +           ++               EE+    S +A  S+EQLE+L
Sbjct: 366 IVDGLVDMDAAEPVVAPPAPAASSDDEEDEEEEEEEEEEEEETTAASGAAGFSSEQLEQL 425

Query: 240 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 299
           K +SL KFS I+  FDKMRKAFEKEGYNS+ Y+KA   ISNE+L IRFTAK +EKLCDTL
Sbjct: 426 KRDSLAKFSTIAQQFDKMRKAFEKEGYNSKPYVKAQEIISNELLSIRFTAKVVEKLCDTL 485

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
           R Q+++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL+WVD E   +H Y+++L RN
Sbjct: 486 RGQVDEVRHIEKQILDVAVNRCGMPRGHFIKVFPGNETNLDWVDGEVNGKHAYSVVLARN 545

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
           +P++KELQQKLI+LQ  +VLPL DLR IN+KM AGEMKARKAKREMTEANLRLVISIAKK
Sbjct: 546 VPTVKELQQKLIDLQARVVLPLPDLRAINKKMAAGEMKARKAKREMTEANLRLVISIAKK 605

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 606 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIP 665

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 666 VHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGD 725

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D+DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 726 DDDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 785

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 786 EEVGKQFDVTRERIRQIEAKALRKLR 811


>gi|340786215|ref|YP_004751680.1| RNA polymerase sigma factor [Collimonas fungivorans Ter331]
 gi|340551482|gb|AEK60857.1| RNA polymerase sigma factor [Collimonas fungivorans Ter331]
          Length = 831

 Score =  925 bits (2390), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 466/639 (72%), Positives = 532/639 (83%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIK+GKERG+LTFSEIND LPE+IID E IE II 
Sbjct: 193  KDAFSSDTEA-SEEELEARRQKLKTLIKMGKERGFLTFSEINDHLPENIIDPEAIEGIIG 251

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V E   D ETL+LS+    + SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 252  TFSDMGIAVYEQAPDAETLLLSDNVATVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 311

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL+AADKI K+EIKIDEIV
Sbjct: 312  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILLAADKIGKDEIKIDEIV 371

Query: 987  DGLIDKN----------------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N                  S++   +  ++  E+     S +A  S EQLE+LK
Sbjct: 372  DGLVDPNQTDEAATASAAATAADEDSDDEEEEEEEDAEEDDASSTSGAAGFSAEQLEQLK 431

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
             ++L KF  IS  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 432  RDALGKFETISTQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLR 491

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V QIE+QIL++ VNKCGMPR HFIKVFP NE NL+WVD E    H Y+ +L RN+
Sbjct: 492  GQVDEVRQIERQILDVAVNKCGMPRPHFIKVFPGNETNLDWVDGEVSGNHAYSTVLSRNV 551

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P++KELQQ+LI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 552  PAVKELQQRLIDLQARVVLPLPDLRGINKKMGAGEKKARMAKREMTEANLRLVISIAKKY 611

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 612  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 671

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 672  HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 731

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 732  DDSHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 791

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 792  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 830



 Score =  906 bits (2342), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 457/627 (72%), Positives = 523/627 (83%), Gaps = 21/627 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIK+GKERG+LTFSEIND LPE+IID E IE I
Sbjct: 191 LLKDAFSSDTEA-SEEELEARRQKLKTLIKMGKERGFLTFSEINDHLPENIIDPEAIEGI 249

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V E   D ETL+LS+    + SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 250 IGTFSDMGIAVYEQAPDAETLLLSDNVATVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 309

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL+AADKI K+EIKIDE
Sbjct: 310 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILLAADKIGKDEIKIDE 369

Query: 195 IVDGLIDKN----------------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEK 238
           IVDGL+D N                  S++   +  ++  E+     S +A  S EQLE+
Sbjct: 370 IVDGLVDPNQTDEAATASAAATAADEDSDDEEEEEEEDAEEDDASSTSGAAGFSAEQLEQ 429

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK ++L KF  IS  FDKMRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDT
Sbjct: 430 LKRDALGKFETISTQFDKMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDT 489

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR Q+++V QIE+QIL++ VNKCGMPR HFIKVFP NE NL+WVD E    H Y+ +L R
Sbjct: 490 LRGQVDEVRQIERQILDVAVNKCGMPRPHFIKVFPGNETNLDWVDGEVSGNHAYSTVLSR 549

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
           N+P++KELQQ+LI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAK
Sbjct: 550 NVPAVKELQQRLIDLQARVVLPLPDLRGINKKMGAGEKKARMAKREMTEANLRLVISIAK 609

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 610 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 669

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+G
Sbjct: 670 PVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIG 729

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHT
Sbjct: 730 DDDDSHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHT 789

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR 625
           LEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 790 LEEVGKQFDVTRERIRQIEAKALRKLR 816


>gi|395763824|ref|ZP_10444493.1| RNA polymerase primary sigma factor [Janthinobacterium lividum PAMC
            25724]
          Length = 746

 Score =  924 bits (2389), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 459/636 (72%), Positives = 527/636 (82%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+I+D E IE II 
Sbjct: 111  KDAFSSDTEA-SEEELERRRQKLKTLIKFGKERGFLTYAEINDHLPENIVDPEAIEGIIG 169

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V EH  D ETL+LS+    +TSDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 170  TFNDMGIAVYEHAPDAETLLLSDNVAVVTSDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 229

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ AAD+I+  EIKIDEIV
Sbjct: 230  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIAAADRIANEEIKIDEIV 289

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIE-------------SSSADLSTEQLEKLKYES 1033
            DGL+D+N       +      ++E+                 S +A  S EQLE LK  +
Sbjct: 290  DGLVDENEPVAAAPVVAAAVEDDEEEGEAEEEEVGEEEEASVSGAAGFSAEQLETLKRTA 349

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGYNS+ Y KA   IS E+LGIRFTAK +EKLCDTLR Q+
Sbjct: 350  LEKFAVISQQFDKMRRAFEKEGYNSKPYAKAQQAISQELLGIRFTAKVVEKLCDTLRGQV 409

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL+WVD E    H Y+ IL RNIP++
Sbjct: 410  DEVRHIEKQILDVAVNRCGMPRAHFIKVFPGNETNLDWVDGEVNAGHAYSAILGRNIPTV 469

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            KELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISIAKKYT+R
Sbjct: 470  KELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISIAKKYTNR 529

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 530  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 589

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG+EPDP+ +A+KMEMPEEKIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 590  ETINKMNRISRQILQETGAEPDPATLAVKMEMPEEKIRKIMKIAKEPISMETPIGDDDDS 649

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 650  HLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 709

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 710  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 745



 Score =  906 bits (2342), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 450/625 (72%), Positives = 518/625 (82%), Gaps = 18/625 (2%)

Query: 18  TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIES 77
            LLK+AFS D ++ S EE+E  R+K K LIK GKERG+LT++EIND LPE+I+D E IE 
Sbjct: 108 ALLKDAFSSDTEA-SEEELERRRQKLKTLIKFGKERGFLTYAEINDHLPENIVDPEAIEG 166

Query: 78  IIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIK 133
           II TF  M I+V EH  D ETL+LS+    +TSDD+ E A EAALSTVDSDFGRT DP++
Sbjct: 167 IIGTFNDMGIAVYEHAPDAETLLLSDNVAVVTSDDEAEAAAEAALSTVDSDFGRTTDPVR 226

Query: 134 MYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKID 193
           MYMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ AAD+I+  EIKID
Sbjct: 227 MYMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIAAADRIANEEIKID 286

Query: 194 EIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE-------------SSSADLSTEQLEKLK 240
           EIVDGL+D+N       +      ++E+                 S +A  S EQLE LK
Sbjct: 287 EIVDGLVDENEPVAAAPVVAAAVEDDEEEGEAEEEEVGEEEEASVSGAAGFSAEQLETLK 346

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
             +L KF+ IS  FDKMR+AFEKEGYNS+ Y KA   IS E+LGIRFTAK +EKLCDTLR
Sbjct: 347 RTALEKFAVISQQFDKMRRAFEKEGYNSKPYAKAQQAISQELLGIRFTAKVVEKLCDTLR 406

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL+WVD E    H Y+ IL RNI
Sbjct: 407 GQVDEVRHIEKQILDVAVNRCGMPRAHFIKVFPGNETNLDWVDGEVNAGHAYSAILGRNI 466

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P++KELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISIAKKY
Sbjct: 467 PTVKELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISIAKKY 526

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 527 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 586

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +A+KMEMPEEKIRKIMKIAKEP+SME+P+GDD
Sbjct: 587 HMIETINKMNRISRQILQETGAEPDPATLAVKMEMPEEKIRKIMKIAKEPISMETPIGDD 646

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 647 DDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 706

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 707 EVGKQFDVTRERIRQIEAKALRKLR 731


>gi|445499114|ref|ZP_21465969.1| RNA polymerase sigma factor RpoD [Janthinobacterium sp. HH01]
 gi|444789109|gb|ELX10657.1| RNA polymerase sigma factor RpoD [Janthinobacterium sp. HH01]
          Length = 746

 Score =  923 bits (2386), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 461/635 (72%), Positives = 527/635 (82%), Gaps = 17/635 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ + EE+E  R+K K LIK GKERG+LT++EIND LPE+I+D E IE II 
Sbjct: 112  KDAFSSDTEA-TEEELERRRQKLKTLIKFGKERGFLTYAEINDHLPENIVDPEAIEGIIG 170

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V EH  D ETL+LS+    +TSDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 171  TFNDMGIAVYEHAPDAETLLLSDNVATVTSDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 230

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ A+D+I  +EIKIDEIV
Sbjct: 231  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIAASDRIRADEIKIDEIV 290

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILI------------ESSSADLSTEQLEKLKYESL 1034
            DGL+D +      V+      +EE+                S +A  S EQLE LK  +L
Sbjct: 291  DGLVDDSEEVAAPVVAAPAEEDEEEEEEEEEEEEEEEEASASGAAGFSAEQLEALKNAAL 350

Query: 1035 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 1094
             KF  IS  FDKMR+AFEKEGYNS++Y+KA   IS E+LGIRFTAK +EKLCDTLR Q++
Sbjct: 351  EKFDVISLQFDKMRRAFEKEGYNSKAYVKAQEAISYELLGIRFTAKVVEKLCDTLRGQVD 410

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
            +V  IEKQIL++ VNKCGMPR HFIKVFP NE NL WVD E    H Y+ IL RNIP+IK
Sbjct: 411  EVRHIEKQILDVAVNKCGMPRAHFIKVFPGNETNLEWVDGEVAAGHAYSAILGRNIPTIK 470

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
            ELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISIAKKYT+RG
Sbjct: 471  ELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISIAKKYTNRG 530

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 531  LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 590

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSH
Sbjct: 591  TINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSH 650

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED N LAPSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGK
Sbjct: 651  LGDFIEDNNTLAPSDAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGK 710

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            QFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 711  QFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 745



 Score =  905 bits (2338), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 452/623 (72%), Positives = 518/623 (83%), Gaps = 17/623 (2%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ + EE+E  R+K K LIK GKERG+LT++EIND LPE+I+D E IE I
Sbjct: 110 LLKDAFSSDTEA-TEEELERRRQKLKTLIKFGKERGFLTYAEINDHLPENIVDPEAIEGI 168

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V EH  D ETL+LS+    +TSDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 169 IGTFNDMGIAVYEHAPDAETLLLSDNVATVTSDDEAEAAAEAALSTVDSDFGRTTDPVRM 228

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ A+D+I  +EIKIDE
Sbjct: 229 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIAASDRIRADEIKIDE 288

Query: 195 IVDGLIDKNFSSNNRVIKGNKNNNEEKILI------------ESSSADLSTEQLEKLKYE 242
           IVDGL+D +      V+      +EE+                S +A  S EQLE LK  
Sbjct: 289 IVDGLVDDSEEVAAPVVAAPAEEDEEEEEEEEEEEEEEEEASASGAAGFSAEQLEALKNA 348

Query: 243 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 302
           +L KF  IS  FDKMR+AFEKEGYNS++Y+KA   IS E+LGIRFTAK +EKLCDTLR Q
Sbjct: 349 ALEKFDVISLQFDKMRRAFEKEGYNSKAYVKAQEAISYELLGIRFTAKVVEKLCDTLRGQ 408

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           +++V  IEKQIL++ VNKCGMPR HFIKVFP NE NL WVD E    H Y+ IL RNIP+
Sbjct: 409 VDEVRHIEKQILDVAVNKCGMPRAHFIKVFPGNETNLEWVDGEVAAGHAYSAILGRNIPT 468

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           IKELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISIAKKYT+
Sbjct: 469 IKELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISIAKKYTN 528

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 529 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 588

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 589 IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 648

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED N LAPSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 649 SHLGDFIEDNNTLAPSDAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 708

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 709 GKQFDVTRERIRQIEAKALRKLR 731


>gi|409404651|ref|ZP_11253130.1| RNA polymerase sigma-70 factor transcription regulator protein
            [Herbaspirillum sp. GW103]
 gi|386436170|gb|EIJ48993.1| RNA polymerase sigma-70 factor transcription regulator protein
            [Herbaspirillum sp. GW103]
          Length = 741

 Score =  921 bits (2380), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 466/637 (73%), Positives = 529/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE II 
Sbjct: 105  KDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIG 163

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 164  TFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 223

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DEIV
Sbjct: 224  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDEIV 283

Query: 987  DGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL+D N S                    +      EE     S +A  S EQLE+LK +
Sbjct: 284  DGLVDPNESEQQVEAASSDSDEDDEEEEEEEEDEEEEENESSGSGAAGFSAEQLEQLKRD 343

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            +L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 344  ALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQ 403

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+P+
Sbjct: 404  VDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNVPA 463

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKYT+
Sbjct: 464  IKELQQKLIDLQARVVLPLPDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTN 523

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 524  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 583

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 584  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 643

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 644  SHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEV 703

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 704  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 740



 Score =  902 bits (2332), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 457/625 (73%), Positives = 520/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE I
Sbjct: 103 LLKDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGI 161

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 162 IGTFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 221

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DE
Sbjct: 222 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDE 281

Query: 195 IVDGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 240
           IVDGL+D N S                    +      EE     S +A  S EQLE+LK
Sbjct: 282 IVDGLVDPNESEQQVEAASSDSDEDDEEEEEEEEDEEEEENESSGSGAAGFSAEQLEQLK 341

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            ++L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 342 RDALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLR 401

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+
Sbjct: 402 AQVDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSAVLSRNV 461

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P+IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 462 PAIKELQQKLIDLQARVVLPLPDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKY 521

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 522 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 581

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 582 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 641

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 642 DDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 701

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 702 EVGKQFDVTRERIRQIEAKALRKLR 726


>gi|427400732|ref|ZP_18891970.1| RNA polymerase sigma factor RpoD [Massilia timonae CCUG 45783]
 gi|425720245|gb|EKU83168.1| RNA polymerase sigma factor RpoD [Massilia timonae CCUG 45783]
          Length = 753

 Score =  921 bits (2380), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 463/641 (72%), Positives = 532/641 (82%), Gaps = 23/641 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R K K LIK GKERG+LT+SEIND LPE+I+D E IE II 
Sbjct: 112  KDAFSSDTEA-SEEELELRRNKLKALIKSGKERGFLTYSEINDHLPENIVDPEAIEGIIG 170

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V EH  D ETL+LS    N+TSDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 171  TFNDMGIAVYEHAPDAETLLLSDNVPNVTSDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 230

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ AA+KI ++EIKIDEIV
Sbjct: 231  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIDAANKIERDEIKIDEIV 290

Query: 987  DGLIDKNF---SSNNRVIKGNKNNNEEKILIE---------------SSSADLSTEQLEK 1028
            DG++D      +S + V   + +++E++   E                ++A  S EQLE 
Sbjct: 291  DGMVDPEEGEETSPSAVAPTSTDSDEDEEDEEDAEEEEEEEEASTGTGAAAGYSAEQLEA 350

Query: 1029 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 1088
            LK  +L KF  I   FDKMRKAFEK+GYNS++Y+KA   ISNE+LGIRFTAK +EKLCDT
Sbjct: 351  LKAAALGKFDEIGQQFDKMRKAFEKDGYNSKAYVKAQEAISNELLGIRFTAKVVEKLCDT 410

Query: 1089 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 1148
            LR Q+++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL WVD E    H Y+ IL R
Sbjct: 411  LRGQVDEVRHIEKQILDVAVNRCGMPRAHFIKVFPGNETNLEWVDGEVDAGHAYSAILGR 470

Query: 1149 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 1208
            NIP+IKELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISIAK
Sbjct: 471  NIPTIKELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISIAK 530

Query: 1209 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268
            KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 531  KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 590

Query: 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328
            PVHMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+G
Sbjct: 591  PVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIG 650

Query: 1329 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 1388
            DD+DSHLGDFIED N LAPSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHT
Sbjct: 651  DDDDSHLGDFIEDNNTLAPSDAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHT 710

Query: 1389 LEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            LEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 711  LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 751



 Score =  902 bits (2332), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 454/629 (72%), Positives = 523/629 (83%), Gaps = 23/629 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R K K LIK GKERG+LT+SEIND LPE+I+D E IE I
Sbjct: 110 LLKDAFSSDTEA-SEEELELRRNKLKALIKSGKERGFLTYSEINDHLPENIVDPEAIEGI 168

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V EH  D ETL+LS    N+TSDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 169 IGTFNDMGIAVYEHAPDAETLLLSDNVPNVTSDDEAEAAAEAALSTVDSDFGRTTDPVRM 228

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CP TI EI+ AA+KI ++EIKIDE
Sbjct: 229 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPVTIAEIIDAANKIERDEIKIDE 288

Query: 195 IVDGLIDK---NFSSNNRVIKGNKNNNEEKILIE---------------SSSADLSTEQL 236
           IVDG++D      +S + V   + +++E++   E                ++A  S EQL
Sbjct: 289 IVDGMVDPEEGEETSPSAVAPTSTDSDEDEEDEEDAEEEEEEEEASTGTGAAAGYSAEQL 348

Query: 237 EKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLC 296
           E LK  +L KF  I   FDKMRKAFEK+GYNS++Y+KA   ISNE+LGIRFTAK +EKLC
Sbjct: 349 EALKAAALGKFDEIGQQFDKMRKAFEKDGYNSKAYVKAQEAISNELLGIRFTAKVVEKLC 408

Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 356
           DTLR Q+++V  IEKQIL++ VN+CGMPR HFIKVFP NE NL WVD E    H Y+ IL
Sbjct: 409 DTLRGQVDEVRHIEKQILDVAVNRCGMPRAHFIKVFPGNETNLEWVDGEVDAGHAYSAIL 468

Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
            RNIP+IKELQQ+LI+LQ  +VLPL DLR+INR+M AGEMKARKAKREMTEANLRLVISI
Sbjct: 469 GRNIPTIKELQQRLIDLQARVVLPLPDLRNINRQMAAGEMKARKAKREMTEANLRLVISI 528

Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
           AKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI
Sbjct: 529 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 588

Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536
           RIPVHMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P
Sbjct: 589 RIPVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETP 648

Query: 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596
           +GDD+DSHLGDFIED N LAPSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+D
Sbjct: 649 IGDDDDSHLGDFIEDNNTLAPSDAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTD 708

Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           HTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 709 HTLEEVGKQFDVTRERIRQIEAKALRKLR 737


>gi|415948074|ref|ZP_11556700.1| Putative sigma 70 factor, RNA polymerase [Herbaspirillum frisingense
            GSF30]
 gi|407757963|gb|EKF67857.1| Putative sigma 70 factor, RNA polymerase [Herbaspirillum frisingense
            GSF30]
          Length = 748

 Score =  920 bits (2379), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 465/637 (72%), Positives = 533/637 (83%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE II 
Sbjct: 112  KDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGIIG 170

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 171  TFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 230

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DEIV
Sbjct: 231  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDEIV 290

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIE--------------SSSADLSTEQLEKLKYE 1032
            DGL+D N S        + ++ +++   E              S +A  S EQLE+LK +
Sbjct: 291  DGLVDPNESEQQVDAAASDSDEDDEEAEEDEEEDEEEESENSGSGAAGFSAEQLEQLKRD 350

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            +L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 351  ALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLRAQ 410

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+P+
Sbjct: 411  VDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSTVLSRNVPA 470

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKYT+
Sbjct: 471  IKELQQKLIDLQARVVLPLPDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTN 530

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 531  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 590

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 591  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 650

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 651  SHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEV 710

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 711  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 747



 Score =  902 bits (2331), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 456/625 (72%), Positives = 524/625 (83%), Gaps = 19/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ S EE+E  R+K K LIKLGKERG+LTFSEIND LPE+I+D E IE I
Sbjct: 110 LLKDAFSSDTEA-SEEELERRRQKLKTLIKLGKERGFLTFSEINDHLPENIVDPEAIEGI 168

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M ISV EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 169 IGTFSDMGISVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 228

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AAD+ISK+EIK+DE
Sbjct: 229 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILAAADRISKDEIKVDE 288

Query: 195 IVDGLIDKNFSSNNRVIKGNKNNNEEKILIE--------------SSSADLSTEQLEKLK 240
           IVDGL+D N S        + ++ +++   E              S +A  S EQLE+LK
Sbjct: 289 IVDGLVDPNESEQQVDAAASDSDEDDEEAEEDEEEDEEEESENSGSGAAGFSAEQLEQLK 348

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            ++L KF+ I   F+ MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 349 RDALGKFAVIGTQFENMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKIVEKLCDTLR 408

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q+++V  +E+QIL++ VNKC MPR HFIKVFP NE+NL+WVD E    HDY+ +L RN+
Sbjct: 409 AQVDEVRTVERQILDVAVNKCNMPRAHFIKVFPGNEVNLDWVDGEVAANHDYSTVLSRNV 468

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P+IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 469 PAIKELQQKLIDLQARVVLPLPDLRAINKKMGAGEKKARMAKREMTEANLRLVISIAKKY 528

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 529 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 588

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 589 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 648

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR+VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 649 DDSHLGDFIEDNNTLAPADAALHASMRNVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 708

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 709 EVGKQFDVTRERIRQIEAKALRKLR 733


>gi|399017721|ref|ZP_10719910.1| RNA polymerase sigma factor, sigma-70 family [Herbaspirillum sp.
            CF444]
 gi|398102488|gb|EJL92668.1| RNA polymerase sigma factor, sigma-70 family [Herbaspirillum sp.
            CF444]
          Length = 747

 Score =  917 bits (2370), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 468/637 (73%), Positives = 529/637 (83%), Gaps = 21/637 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ + EE+E  R+K K LIK GKERG+LTFSEIND LPE+I+D E IE II 
Sbjct: 113  KDAFSSDTEA-TEEELERRRQKLKTLIKQGKERGFLTFSEINDHLPENIVDPEAIEGIIG 171

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++MYM
Sbjct: 172  TFNDMGIAVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRMYM 231

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL+AADKI  +EIK+DEIV
Sbjct: 232  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILVAADKIKNDEIKVDEIV 291

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD--------------LSTEQLEKLKYE 1032
            DGL+D   S    V+    ++ EE    E    D               S EQLE+LK +
Sbjct: 292  DGLVD--MSEGEVVVAAAASDEEEDEEDEDEEEDEEEEGESSGSGAAGFSAEQLEQLKRD 349

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            +L KF+ IS  FD MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR Q
Sbjct: 350  ALGKFATISTQFDNMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLRGQ 409

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            ++QV QIE+QIL++ VNKC MPR HFIKVFP NEINL+WVD E    HDY+ +L RN+P+
Sbjct: 410  VDQVRQIERQILDVAVNKCNMPRTHFIKVFPGNEINLDWVDGEVSANHDYSTVLSRNVPA 469

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKYT+
Sbjct: 470  IKELQQKLIDLQARVVLPLPDLRGINKKMGAGEKKARMAKREMTEANLRLVISIAKKYTN 529

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 530  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 589

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 590  IETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 649

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 650  SHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEV 709

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 710  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 746



 Score =  899 bits (2322), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 459/625 (73%), Positives = 521/625 (83%), Gaps = 21/625 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ + EE+E  R+K K LIK GKERG+LTFSEIND LPE+I+D E IE I
Sbjct: 111 LLKDAFSSDTEA-TEEELERRRQKLKTLIKQGKERGFLTFSEINDHLPENIVDPEAIEGI 169

Query: 79  IKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V EH  D ETL+LS    N+ SDDD E A EAALSTVDSDFGRT DP++M
Sbjct: 170 IGTFNDMGIAVYEHAPDAETLLLSDNVANVASDDDAEAAAEAALSTVDSDFGRTTDPVRM 229

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL+AADKI  +EIK+DE
Sbjct: 230 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTIAEILVAADKIKNDEIKVDE 289

Query: 195 IVDGLIDKNFSSNNRVI--------------KGNKNNNEEKILIESSSADLSTEQLEKLK 240
           IVDGL+D   S    V+                 ++  EE     S +A  S EQLE+LK
Sbjct: 290 IVDGLVD--MSEGEVVVAAAASDEEEDEEDEDEEEDEEEEGESSGSGAAGFSAEQLEQLK 347

Query: 241 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            ++L KF+ IS  FD MRKAFEKEGYNS+ Y+KA   ISNE+LGIRFTAK +EKLCDTLR
Sbjct: 348 RDALGKFATISTQFDNMRKAFEKEGYNSKPYVKAQEIISNELLGIRFTAKVVEKLCDTLR 407

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
            Q++QV QIE+QIL++ VNKC MPR HFIKVFP NEINL+WVD E    HDY+ +L RN+
Sbjct: 408 GQVDQVRQIERQILDVAVNKCNMPRTHFIKVFPGNEINLDWVDGEVSANHDYSTVLSRNV 467

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
           P+IKELQQKLI+LQ  +VLPL DLR IN+KM AGE KAR AKREMTEANLRLVISIAKKY
Sbjct: 468 PAIKELQQKLIDLQARVVLPLPDLRGINKKMGAGEKKARMAKREMTEANLRLVISIAKKY 527

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 528 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 587

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 588 HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDD 647

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           +DSHLGDFIED N LAP+DAAL+ASMR VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 648 DDSHLGDFIEDNNTLAPADAALHASMRGVVKDILDSLTPREAKVLRMRFGIEMSTDHTLE 707

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 708 EVGKQFDVTRERIRQIEAKALRKLR 732


>gi|329906288|ref|ZP_08274384.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
            IMCC9480]
 gi|327547308|gb|EGF32147.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
            IMCC9480]
          Length = 827

 Score =  916 bits (2368), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 450/639 (70%), Positives = 528/639 (82%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS D ++ + EE+E  R+K K LIKLGK+RG+LT++EIND LPE+I+D E IE II 
Sbjct: 189  KDAFSSDTEA-TEEELERRRQKLKTLIKLGKDRGFLTYAEINDHLPENIVDPEAIEGIIG 247

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V EH  D E+++L++    + SDD+ E A EAALSTVDSDFGRT DP++MYM
Sbjct: 248  TFNDMGIAVYEHAPDAESMLLTDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRMYM 307

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AA++I+  E KIDEIV
Sbjct: 308  REMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTISEILAAAERITNGETKIDEIV 367

Query: 987  DGLID----------------KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D                ++           + +  E+    S +A  + EQ+E+LK
Sbjct: 368  DGLVDMLVIEVVVVPPPKVVSEDDEEEEEEEAEEEESGAEEETNASGAAGFTAEQIEQLK 427

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
             ESL+KF  IS  FDKMRKA+EKEGYNS+ Y+KA   IS+E+L IRFTAK +EKLCDTLR
Sbjct: 428  RESLVKFQAISTQFDKMRKAYEKEGYNSKPYVKAQEAISSELLAIRFTAKVVEKLCDTLR 487

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+ +V  IE+QIL++ VNKC MPR HFIKVFP NE NL+WVD E    H Y++IL RN+
Sbjct: 488  GQVEEVRHIERQILDVAVNKCRMPRSHFIKVFPGNETNLDWVDGEVSGNHPYSVILGRNV 547

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P++KELQQKL++LQ+ +VLPL DLR INR+M AGEMKARKAKREMTEANLRLVISIAKKY
Sbjct: 548  PTVKELQQKLLDLQSRVVLPLPDLRAINRRMAAGEMKARKAKREMTEANLRLVISIAKKY 607

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 608  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 667

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG+EPDP+ +AIKMEMPEEKIRKIMKIAKEP+SME+P+GDD
Sbjct: 668  HMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEEKIRKIMKIAKEPISMETPIGDD 727

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 728  DDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 787

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  +LK FLEG
Sbjct: 788  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDRLKSFLEG 826



 Score =  899 bits (2322), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/627 (70%), Positives = 519/627 (82%), Gaps = 21/627 (3%)

Query: 19  LLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 78
           LLK+AFS D ++ + EE+E  R+K K LIKLGK+RG+LT++EIND LPE+I+D E IE I
Sbjct: 187 LLKDAFSSDTEA-TEEELERRRQKLKTLIKLGKDRGFLTYAEINDHLPENIVDPEAIEGI 245

Query: 79  IKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKM 134
           I TF  M I+V EH  D E+++L++    + SDD+ E A EAALSTVDSDFGRT DP++M
Sbjct: 246 IGTFNDMGIAVYEHAPDAESMLLTDNVATVASDDEAEAAAEAALSTVDSDFGRTTDPVRM 305

Query: 135 YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 194
           YMREMGSVELLTR+GEIEIAKRIE+GLKDMI AIS+CPTTI EIL AA++I+  E KIDE
Sbjct: 306 YMREMGSVELLTREGEIEIAKRIEDGLKDMIQAISACPTTISEILAAAERITNGETKIDE 365

Query: 195 IVDGLID----------------KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEK 238
           IVDGL+D                ++           + +  E+    S +A  + EQ+E+
Sbjct: 366 IVDGLVDMLVIEVVVVPPPKVVSEDDEEEEEEEAEEEESGAEEETNASGAAGFTAEQIEQ 425

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK ESL+KF  IS  FDKMRKA+EKEGYNS+ Y+KA   IS+E+L IRFTAK +EKLCDT
Sbjct: 426 LKRESLVKFQAISTQFDKMRKAYEKEGYNSKPYVKAQEAISSELLAIRFTAKVVEKLCDT 485

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR Q+ +V  IE+QIL++ VNKC MPR HFIKVFP NE NL+WVD E    H Y++IL R
Sbjct: 486 LRGQVEEVRHIERQILDVAVNKCRMPRSHFIKVFPGNETNLDWVDGEVSGNHPYSVILGR 545

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
           N+P++KELQQKL++LQ+ +VLPL DLR INR+M AGEMKARKAKREMTEANLRLVISIAK
Sbjct: 546 NVPTVKELQQKLLDLQSRVVLPLPDLRAINRRMAAGEMKARKAKREMTEANLRLVISIAK 605

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 606 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 665

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQILQETG+EPDP+ +AIKMEMPEEKIRKIMKIAKEP+SME+P+G
Sbjct: 666 PVHMIETINKMNRISRQILQETGAEPDPATLAIKMEMPEEKIRKIMKIAKEPISMETPIG 725

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED N LAP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHT
Sbjct: 726 DDDDSHLGDFIEDNNTLAPADAALHASMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHT 785

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR 625
           LEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 786 LEEVGKQFDVTRERIRQIEAKALRKLR 812


>gi|237746700|ref|ZP_04577180.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
 gi|229378051|gb|EEO28142.1| RNA polymerase primary sigma factor [Oxalobacter formigenes HOxBLS]
          Length = 827

 Score =  867 bits (2239), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 426/622 (68%), Positives = 513/622 (82%), Gaps = 29/622 (4%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K+LIKLGKER +LT++EIND LP+++ID + IE II TF  M ISV EH  D E L+L++
Sbjct: 206  KMLIKLGKERSFLTYAEINDHLPDNVIDPDAIEGIISTFNDMGISVYEHAPDAEDLLLTD 265

Query: 894  ----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
                +TSD++ E A EAALSTVDSDFGRT DP++MYMREMGSVELLTR+GEIEIAKRIEE
Sbjct: 266  NVVTVTSDEEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEE 325

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG------ 1003
            GLKDMI AISSCPTTI+EI+  A+KI  +EI+IDE+VDGL D+  +  ++V+        
Sbjct: 326  GLKDMIQAISSCPTTILEIIGQAEKIRNDEIRIDEVVDGLADE--AGESQVLAAASDNDQ 383

Query: 1004 -----------------NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
                              +    +      ++A  S EQLEKLK ++L +F+ I  +F +
Sbjct: 384  DESDEDDSDADENDGEEAEEEESDGGSAGGAAAGFSAEQLEKLKEDALARFALIETYFKE 443

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M++AFEK+GYNS +Y+KAHN+IS+E+LG+RFTA+ IEKLCDTLR Q++ V QIE++IL +
Sbjct: 444  MQQAFEKDGYNSPAYVKAHNSISDELLGMRFTARFIEKLCDTLRTQMDDVRQIEREILNV 503

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             VNKCG+PR HFIK FP NE N+ WVD E    H Y+ IL RN+P IKELQQ L++++  
Sbjct: 504  AVNKCGVPRAHFIKTFPGNETNMEWVDEEVHAGHPYSEILSRNVPMIKELQQNLVDIEKR 563

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
            I +PL DLR+INRKM+AGEM+ARKAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 564  IGMPLADLREINRKMVAGEMRARKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 623

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQI
Sbjct: 624  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 683

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG+EPDP+ +A+KM+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N LA
Sbjct: 684  LQETGAEPDPATLAVKMDMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLA 743

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P+DAAL+ASMR+VVKD+L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQI
Sbjct: 744  PADAALHASMRNVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQI 803

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR  KLK FLE
Sbjct: 804  EAKALRKLRHPSRSDKLKSFLE 825



 Score =  854 bits (2207), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 430/647 (66%), Positives = 528/647 (81%), Gaps = 31/647 (4%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K + K++K KE  LLK+A + D ++ + EE+E  R++ K+LIKLGKER +LT++EIND L
Sbjct: 169 KARAKDRKAKEKALLKDALAGDTEA-TEEELERRRERLKMLIKLGKERSFLTYAEINDHL 227

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+++ID + IE II TF  M ISV EH  D E L+L++    +TSD++ E A EAALSTV
Sbjct: 228 PDNVIDPDAIEGIISTFNDMGISVYEHAPDAEDLLLTDNVVTVTSDEEAEAAAEAALSTV 287

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DSDFGRT DP++MYMREMGSVELLTR+GEIEIAKRIEEGLKDMI AISSCPTTI+EI+  
Sbjct: 288 DSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEGLKDMIQAISSCPTTILEIIGQ 347

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG-----------------------NKNNN 218
           A+KI  +EI+IDE+VDGL D+  +  ++V+                          +   
Sbjct: 348 AEKIRNDEIRIDEVVDGLADE--AGESQVLAAASDNDQDESDEDDSDADENDGEEAEEEE 405

Query: 219 EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278
            +      ++A  S EQLEKLK ++L +F+ I  +F +M++AFEK+GYNS +Y+KAHN+I
Sbjct: 406 SDGGSAGGAAAGFSAEQLEKLKEDALARFALIETYFKEMQQAFEKDGYNSPAYVKAHNSI 465

Query: 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 338
           S+E+LG+RFTA+ IEKLCDTLR Q++ V QIE++IL + VNKCG+PR HFIK FP NE N
Sbjct: 466 SDELLGMRFTARFIEKLCDTLRTQMDDVRQIEREILNVAVNKCGVPRAHFIKTFPGNETN 525

Query: 339 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
           + WVD E    H Y+ IL RN+P IKELQQ L++++  I +PL DLR+INRKM+AGEM+A
Sbjct: 526 MEWVDEEVHAGHPYSEILSRNVPMIKELQQNLVDIEKRIGMPLADLREINRKMVAGEMRA 585

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           RKAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 586 RKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 645

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A+KM+MPE+
Sbjct: 646 WWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAVKMDMPED 705

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N LAP+DAAL+ASMR+VVKD+L+SLT
Sbjct: 706 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRNVVKDVLDSLT 765

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           PRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 766 PREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 812


>gi|237748836|ref|ZP_04579316.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
 gi|229380198|gb|EEO30289.1| RNA polymerase primary sigma factor [Oxalobacter formigenes OXCC13]
          Length = 819

 Score =  866 bits (2237), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 428/618 (69%), Positives = 513/618 (83%), Gaps = 24/618 (3%)

Query: 835  ILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN- 893
            ILIKLGKER +LT++EIND LP+++ID + IE II TF  M ISV E   D E L+L++ 
Sbjct: 200  ILIKLGKERSFLTYAEINDHLPDNVIDPDAIEGIISTFNDMGISVYEQAPDAEELLLTDN 259

Query: 894  ---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
               +TSD++ E A EAALSTVDSDFGRT DP++MYMREMGSVELLTR+GEIEIAKRIEEG
Sbjct: 260  VVTVTSDEEAEAAAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEG 319

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            L+DMI AISSCPTTI+EI+  A+KI  +E+KIDE+VDGL D    S N  +  + ++++E
Sbjct: 320  LRDMISAISSCPTTILEIIDQAEKIRADEVKIDEVVDGLADDEEGSENAALNASASDSDE 379

Query: 1011 KILIESSSADLSTE--------------------QLEKLKYESLIKFSNISFHFDKMRKA 1050
                E S  + S +                    QLEKLK E+L KF+ I  HF +M+++
Sbjct: 380  DSDEEDSDEEDSDDEEDDEESGSAGGAAAGFSAEQLEKLKDEALGKFAVIGAHFKEMQQS 439

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            FEK+GYNS +Y++AH +IS E+L +RFTA+ IEKLCDTLR Q+++V QIE++IL +VVNK
Sbjct: 440  FEKDGYNSPAYLQAHESISAELLTMRFTARFIEKLCDTLRAQMDEVRQIEREILNVVVNK 499

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            CG+PR HFIK FP NE +L W+D E +  H Y+ IL RN+P +KELQQKL+++Q  I +P
Sbjct: 500  CGVPRAHFIKTFPGNETDLTWIDEEVEADHPYSAILERNVPMVKELQQKLVDIQNRIGMP 559

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L DLR+INRKM+AGEM+ARKAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 560  LADLREINRKMVAGEMRARKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 619

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 620  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 679

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G+EPDP+ +A+KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N LAPSDA
Sbjct: 680  GAEPDPATLAVKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPSDA 739

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            AL+ASMR+VVKD+L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 740  ALHASMRNVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKA 799

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR  KLK FLE
Sbjct: 800  LRKLRHPSRSDKLKSFLE 817



 Score =  854 bits (2207), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 436/650 (67%), Positives = 532/650 (81%), Gaps = 27/650 (4%)

Query: 1   MKFINKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFS 59
           MK ++K  + K++K KE  LLK+A S D ++ S EE+E  R++  ILIKLGKER +LT++
Sbjct: 157 MKAVDK-ARAKDRKAKEKALLKDALSGDSEA-SMEELERRRERLMILIKLGKERSFLTYA 214

Query: 60  EINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATE 115
           EIND LP+++ID + IE II TF  M ISV E   D E L+L++    +TSD++ E A E
Sbjct: 215 EINDHLPDNVIDPDAIEGIISTFNDMGISVYEQAPDAEELLLTDNVVTVTSDEEAEAAAE 274

Query: 116 AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTI 175
           AALSTVDSDFGRT DP++MYMREMGSVELLTR+GEIEIAKRIEEGL+DMI AISSCPTTI
Sbjct: 275 AALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEGLRDMISAISSCPTTI 334

Query: 176 MEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTE- 234
           +EI+  A+KI  +E+KIDE+VDGL D    S N  +  + ++++E    E S  + S + 
Sbjct: 335 LEIIDQAEKIRADEVKIDEVVDGLADDEEGSENAALNASASDSDEDSDEEDSDEEDSDDE 394

Query: 235 -------------------QLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
                              QLEKLK E+L KF+ I  HF +M+++FEK+GYNS +Y++AH
Sbjct: 395 EDDEESGSAGGAAAGFSAEQLEKLKDEALGKFAVIGAHFKEMQQSFEKDGYNSPAYLQAH 454

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
            +IS E+L +RFTA+ IEKLCDTLR Q+++V QIE++IL +VVNKCG+PR HFIK FP N
Sbjct: 455 ESISAELLTMRFTARFIEKLCDTLRAQMDEVRQIEREILNVVVNKCGVPRAHFIKTFPGN 514

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E +L W+D E +  H Y+ IL RN+P +KELQQKL+++Q  I +PL DLR+INRKM+AGE
Sbjct: 515 ETDLTWIDEEVEADHPYSAILERNVPMVKELQQKLVDIQNRIGMPLADLREINRKMVAGE 574

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
           M+ARKAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 575 MRARKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 634

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A+KMEM
Sbjct: 635 YATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAVKMEM 694

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N LAPSDAAL+ASMR+VVKD+L+
Sbjct: 695 PEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPSDAALHASMRNVVKDVLD 754

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 755 SLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 804


>gi|452124047|ref|ZP_21936631.1| RNA polymerase sigma factor RpoD [Bordetella holmesii F627]
 gi|452127433|ref|ZP_21940014.1| RNA polymerase sigma factor RpoD [Bordetella holmesii H558]
 gi|451923277|gb|EMD73418.1| RNA polymerase sigma factor RpoD [Bordetella holmesii F627]
 gi|451926713|gb|EMD76843.1| RNA polymerase sigma factor RpoD [Bordetella holmesii H558]
          Length = 756

 Score =  861 bits (2225), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/613 (67%), Positives = 499/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 147  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 206

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 207  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 266

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL  A ++ +++ +IDE+VDGL+D     +
Sbjct: 267  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHATRVRESQAQIDEVVDGLVD---PED 323

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G   + +E    +  +  +S++QLE L+ ++L KF  +S  FD+MR+++EK+GY 
Sbjct: 324  GEEYAGAGVSADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFDRMRQSYEKDGYR 383

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            SE Y+ A   I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 384  SEIYVTAQETIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRSH 443

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+KVFP NE NL W+  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 444  FLKVFPGNETNLQWIIEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 503

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 504  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 563

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 564  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 623

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 624  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 683

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 684  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 743

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 744  SRADKLKSFLEGQ 756



 Score =  838 bits (2166), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 400/598 (66%), Positives = 487/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 147 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 206

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 207 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 266

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL  A ++ +++ +IDE+VDGL+D     +
Sbjct: 267 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHATRVRESQAQIDEVVDGLVD---PED 323

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G   + +E    +  +  +S++QLE L+ ++L KF  +S  FD+MR+++EK+GY 
Sbjct: 324 GEEYAGAGVSADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFDRMRQSYEKDGYR 383

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           SE Y+ A   I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 384 SEIYVTAQETIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRSH 443

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+KVFP NE NL W+  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 444 FLKVFPGNETNLQWIIEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 503

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 504 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 563

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 564 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 623

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 624 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 683

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 684 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 741


>gi|359798951|ref|ZP_09301520.1| RNA polymerase sigma factor RpoD [Achromobacter arsenitoxydans SY8]
 gi|359363089|gb|EHK64817.1| RNA polymerase sigma factor RpoD [Achromobacter arsenitoxydans SY8]
          Length = 755

 Score =  858 bits (2217), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/611 (67%), Positives = 497/611 (81%), Gaps = 7/611 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 148  EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 207

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 208  PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 267

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 268  EIEIAKRIEDGLKHMVMAISACPTTINEILAHIMRVREGQAQIDEVVDGLVD---PEDGE 324

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
               G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY S+
Sbjct: 325  EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSD 384

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPRLHFI
Sbjct: 385  IYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRLHFI 444

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            KVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 445  KVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 504

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 505  RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 564

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 565  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 624

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 625  AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 684

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 685  VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 744

Query: 1420 YYKLKIFLEGK 1430
              KLK FLEG+
Sbjct: 745  ADKLKSFLEGQ 755



 Score =  836 bits (2159), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/596 (66%), Positives = 485/596 (81%), Gaps = 7/596 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 148 EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 207

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 208 PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 267

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 268 EIEIAKRIEDGLKHMVMAISACPTTINEILAHIMRVREGQAQIDEVVDGLVD---PEDGE 324

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
              G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY S+
Sbjct: 325 EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSD 384

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPRLHFI
Sbjct: 385 IYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRLHFI 444

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           KVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 445 KVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 504

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 505 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 564

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 565 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 624

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 625 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 684

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 685 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>gi|187478819|ref|YP_786843.1| RNA polymerase sigma factor RpoD [Bordetella avium 197N]
 gi|115423405|emb|CAJ49939.1| RNA polymerase sigma factor 70 [Bordetella avium 197N]
          Length = 726

 Score =  858 bits (2216), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/613 (67%), Positives = 498/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 117  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 176

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 177  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 236

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL  A ++ + + +IDE+VDGL+D     +
Sbjct: 237  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHATRVREGQNQIDEVVDGLVD---PED 293

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G   + +E+   +  +  +S++QLE L+ ++L KF  +S  FDKMR ++EK+GY 
Sbjct: 294  GEEYAGAGVSADEEEGDDGPAGGMSSKQLEDLRVKALAKFDEVSRQFDKMRNSYEKDGYR 353

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+ YI A   I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 354  SDIYISAQETIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRSH 413

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+KVFP NE NL WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 414  FLKVFPGNETNLQWVVEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 473

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 474  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 533

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 534  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 593

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 594  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 653

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 654  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 713

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 714  SRADKLKSFLEGQ 726



 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/598 (67%), Positives = 486/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 117 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 176

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 177 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 236

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL  A ++ + + +IDE+VDGL+D     +
Sbjct: 237 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHATRVREGQNQIDEVVDGLVD---PED 293

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G   + +E+   +  +  +S++QLE L+ ++L KF  +S  FDKMR ++EK+GY 
Sbjct: 294 GEEYAGAGVSADEEEGDDGPAGGMSSKQLEDLRVKALAKFDEVSRQFDKMRNSYEKDGYR 353

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S+ YI A   I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 354 SDIYISAQETIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRSH 413

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+KVFP NE NL WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 414 FLKVFPGNETNLQWVVEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 473

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 474 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 533

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 534 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 593

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 594 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 653

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 654 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 711


>gi|423016766|ref|ZP_17007487.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans AXX-A]
 gi|338780194|gb|EGP44609.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans AXX-A]
          Length = 755

 Score =  857 bits (2215), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 146  SAEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 205

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 206  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 265

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 266  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQAQIDEVVDGLVD---PED 322

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY 
Sbjct: 323  GEEYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYK 382

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+ Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 383  SDIYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTH 442

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FIKVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 443  FIKVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 502

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 503  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 562

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 563  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 622

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 623  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 682

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 683  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 742

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 743  SRADKLKSFLEGQ 755



 Score =  835 bits (2156), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 146 SAEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 205

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 206 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 265

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 266 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQAQIDEVVDGLVD---PED 322

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY 
Sbjct: 323 GEEYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYK 382

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S+ Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR H
Sbjct: 383 SDIYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTH 442

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIKVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 443 FIKVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 502

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 503 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 562

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 563 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 622

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR
Sbjct: 623 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMR 682

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 683 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>gi|293604556|ref|ZP_06686961.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
            piechaudii ATCC 43553]
 gi|292817137|gb|EFF76213.1| DNA-directed RNA polymerase sigma subunit RpoD [Achromobacter
            piechaudii ATCC 43553]
          Length = 770

 Score =  857 bits (2213), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/611 (66%), Positives = 496/611 (81%), Gaps = 7/611 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 163  EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 222

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 223  PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 282

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 283  EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 339

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
               G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY S+
Sbjct: 340  EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSD 399

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 400  IYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTHFI 459

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            KVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 460  KVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 519

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 520  RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 579

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 580  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 639

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 640  AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 699

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 700  VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 759

Query: 1420 YYKLKIFLEGK 1430
              KLK FLEG+
Sbjct: 760  ADKLKSFLEGQ 770



 Score =  834 bits (2154), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/596 (66%), Positives = 484/596 (81%), Gaps = 7/596 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 163 EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 222

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 223 PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 282

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 283 EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 339

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
              G     +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+GY S+
Sbjct: 340 EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDGYKSD 399

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 400 IYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTHFI 459

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           KVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 460 KVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 519

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 520 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 579

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 580 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 639

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 640 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 699

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 700 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 755


>gi|33597397|ref|NP_885040.1| RNA polymerase sigma factor RpoD [Bordetella parapertussis 12822]
 gi|33573824|emb|CAE38132.1| RNA polymerase sigma factor 70 [Bordetella parapertussis]
          Length = 760

 Score =  856 bits (2212), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 151  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 210

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 211  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 270

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 271  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 327

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 328  GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 387

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 388  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 447

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 448  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 507

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 508  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 567

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 568  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 627

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 628  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 687

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 688  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 747

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 748  SRADKLKSFLEGQ 760



 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 151 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 210

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 211 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 270

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 271 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 327

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 328 GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 387

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 388 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 447

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 448 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 507

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 508 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 567

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 568 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 627

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 628 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 687

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 688 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 745


>gi|421482971|ref|ZP_15930550.1| RNA polymerase sigma factor RpoD [Achromobacter piechaudii HLE]
 gi|400198775|gb|EJO31732.1| RNA polymerase sigma factor RpoD [Achromobacter piechaudii HLE]
          Length = 756

 Score =  855 bits (2210), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/611 (66%), Positives = 496/611 (81%), Gaps = 7/611 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 149  EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 208

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 209  PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 268

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 269  EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 325

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
               G     +E    +  +  +S++QLE L+ ++L KF  ++  FDKMR ++EK+GY S+
Sbjct: 326  EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVNKQFDKMRLSYEKDGYKSD 385

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 386  VYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTHFI 445

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            KVFP NE NL WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 446  KVFPGNETNLQWVVEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 505

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 506  RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 565

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 566  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 625

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 626  AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 685

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 686  VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 745

Query: 1420 YYKLKIFLEGK 1430
              KLK FLEG+
Sbjct: 746  ADKLKSFLEGQ 756



 Score =  833 bits (2151), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/596 (66%), Positives = 484/596 (81%), Gaps = 7/596 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 149 EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 208

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 209 PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 268

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 269 EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 325

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
              G     +E    +  +  +S++QLE L+ ++L KF  ++  FDKMR ++EK+GY S+
Sbjct: 326 EYAGAGVTADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVNKQFDKMRLSYEKDGYKSD 385

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 386 VYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPRTHFI 445

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           KVFP NE NL WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 446 KVFPGNETNLQWVVEEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 505

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 506 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 565

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 566 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 625

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 626 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 685

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 686 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 741


>gi|33593188|ref|NP_880832.1| RNA polymerase sigma factor RpoD [Bordetella pertussis Tohama I]
 gi|384204485|ref|YP_005590224.1| RNA polymerase sigma factor RpoD [Bordetella pertussis CS]
 gi|408415636|ref|YP_006626343.1| RNA polymerase sigma factor 70 [Bordetella pertussis 18323]
 gi|33563563|emb|CAE42462.1| RNA polymerase sigma factor 70 [Bordetella pertussis Tohama I]
 gi|332382599|gb|AEE67446.1| RNA polymerase sigma factor RpoD [Bordetella pertussis CS]
 gi|401777806|emb|CCJ63147.1| RNA polymerase sigma factor 70 [Bordetella pertussis 18323]
          Length = 760

 Score =  855 bits (2209), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 151  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 210

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 211  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 270

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 271  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 327

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 328  GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 387

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 388  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 447

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 448  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 507

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 508  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 567

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 568  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 627

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 628  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 687

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 688  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 747

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 748  SRADKLKSFLEGQ 760



 Score =  832 bits (2150), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 151 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 210

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 211 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 270

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 271 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 327

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 328 GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 387

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 388 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 447

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 448 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 507

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 508 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 567

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 568 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 627

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 628 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 687

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 688 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 745


>gi|163856346|ref|YP_001630644.1| RNA polymerase sigma factor RpoD [Bordetella petrii DSM 12804]
 gi|163260074|emb|CAP42375.1| RNA polymerase sigma-70 factor [Bordetella petrii]
          Length = 806

 Score =  855 bits (2209), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/615 (66%), Positives = 501/615 (81%), Gaps = 11/615 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 197  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 256

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 257  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 316

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D      
Sbjct: 317  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVDPEDGEE 376

Query: 998  --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
                 +  +++ N++       +  +S++QLE L+ ++L KF  ++  F+KMR+++E++G
Sbjct: 377  YAGAGVAADEDENDD-----GPAGGMSSKQLEDLRVKALAKFDEVTKQFEKMRQSYERDG 431

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y SE+YIKA   I NE++GIRFTAK +EKL DTLR+Q+ +V Q+E+ +L   V++ GMPR
Sbjct: 432  YKSEAYIKAQEAILNELMGIRFTAKMVEKLADTLRSQVEEVRQLERAVLHTCVDRAGMPR 491

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             HFIKVFP NE NL+WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+
Sbjct: 492  SHFIKVFPGNETNLDWVLQEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLK 551

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            D+N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 552  DVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 611

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPD
Sbjct: 612  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 671

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ S
Sbjct: 672  PATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGS 731

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            MR VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 732  MRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 791

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  KLK FLEG+
Sbjct: 792  HPSRADKLKSFLEGQ 806



 Score =  833 bits (2151), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/600 (66%), Positives = 489/600 (81%), Gaps = 11/600 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 197 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 256

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 257 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 316

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D      
Sbjct: 317 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVDPEDGEE 376

Query: 208 --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
                +  +++ N++       +  +S++QLE L+ ++L KF  ++  F+KMR+++E++G
Sbjct: 377 YAGAGVAADEDENDD-----GPAGGMSSKQLEDLRVKALAKFDEVTKQFEKMRQSYERDG 431

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           Y SE+YIKA   I NE++GIRFTAK +EKL DTLR+Q+ +V Q+E+ +L   V++ GMPR
Sbjct: 432 YKSEAYIKAQEAILNELMGIRFTAKMVEKLADTLRSQVEEVRQLERAVLHTCVDRAGMPR 491

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            HFIKVFP NE NL+WV  E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+
Sbjct: 492 SHFIKVFPGNETNLDWVLQEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLK 551

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           D+N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 552 DVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 611

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPD
Sbjct: 612 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 671

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ S
Sbjct: 672 PATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGS 731

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MR VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 732 MRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 791


>gi|311105374|ref|YP_003978227.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
 gi|310760063|gb|ADP15512.1| RNA polymerase sigma factor RpoD [Achromobacter xylosoxidans A8]
          Length = 750

 Score =  853 bits (2204), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/611 (66%), Positives = 495/611 (81%), Gaps = 7/611 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 143  EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 202

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 203  PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 262

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 263  EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 319

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
               G     EE    +  +  +S++QLE L+ ++L KF  +   F+KMR ++EK+GY S+
Sbjct: 320  EYAGAGVTAEEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFEKMRHSYEKDGYKSD 379

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             Y++A  +I NE++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 380  VYVRAQESIQNELMGIRFTAKMVEKLADTLRQQVEEVRQLERAVLHTCVDRAGMPRTHFI 439

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            KVFP NE N+ WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 440  KVFPGNETNMQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 499

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 500  RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 559

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 560  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 619

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 620  AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 679

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 680  VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 739

Query: 1420 YYKLKIFLEGK 1430
              KLK FLEG+
Sbjct: 740  ADKLKSFLEGQ 750



 Score =  831 bits (2146), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/596 (66%), Positives = 483/596 (81%), Gaps = 7/596 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 143 EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 202

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 203 PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 262

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 263 EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 319

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
              G     EE    +  +  +S++QLE L+ ++L KF  +   F+KMR ++EK+GY S+
Sbjct: 320 EYAGAGVTAEEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFEKMRHSYEKDGYKSD 379

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            Y++A  +I NE++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR HFI
Sbjct: 380 VYVRAQESIQNELMGIRFTAKMVEKLADTLRQQVEEVRQLERAVLHTCVDRAGMPRTHFI 439

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           KVFP NE N+ WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 440 KVFPGNETNMQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDVNK 499

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 500 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 559

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 560 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 619

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ SMR V
Sbjct: 620 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGSMRDV 679

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 680 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 735


>gi|1905967|gb|AAC45085.1| RNA polymerase sigma 80 subunit [Bordetella pertussis 18323]
          Length = 733

 Score =  853 bits (2203), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 124  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 183

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 184  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 243

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 244  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 300

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 301  GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 360

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 361  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 420

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 421  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 480

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 481  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 540

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 541  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 600

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 601  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 660

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 661  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 720

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 721  SRADKLKSFLEGQ 733



 Score =  830 bits (2144), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 124 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 183

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 184 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 243

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 244 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 300

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 301 GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 360

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 361 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 420

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 421 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 480

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 481 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 540

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 541 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 600

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 601 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 660

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 661 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 718


>gi|33602137|ref|NP_889697.1| RNA polymerase sigma factor RpoD [Bordetella bronchiseptica RB50]
 gi|427814238|ref|ZP_18981302.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica 1289]
 gi|33576575|emb|CAE33653.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica RB50]
 gi|410565238|emb|CCN22791.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica 1289]
          Length = 722

 Score =  852 bits (2201), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 290  GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 650  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 709

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 710  SRADKLKSFLEGQ 722



 Score =  830 bits (2143), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 290 GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 650 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 707


>gi|410419779|ref|YP_006900228.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica MO149]
 gi|427821294|ref|ZP_18988357.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica D445]
 gi|427821821|ref|ZP_18988883.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica Bbr77]
 gi|408447074|emb|CCJ58746.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica MO149]
 gi|410572294|emb|CCN20565.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica D445]
 gi|410587086|emb|CCN02116.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica Bbr77]
          Length = 722

 Score =  852 bits (2200), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/613 (66%), Positives = 497/613 (81%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 290  GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590  TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 650  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 709

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 710  SRADKLKSFLEGQ 722



 Score =  829 bits (2142), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 485/598 (81%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY 
Sbjct: 290 GEEYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590 TLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 650 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 707


>gi|410473467|ref|YP_006896748.1| RNA polymerase sigma factor 70 [Bordetella parapertussis Bpp5]
 gi|408443577|emb|CCJ50246.1| RNA polymerase sigma factor 70 [Bordetella parapertussis Bpp5]
          Length = 722

 Score =  850 bits (2195), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/613 (66%), Positives = 495/613 (80%), Gaps = 7/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113  SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173  QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233  EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                 G     +E    +  +  +S++QLE L+  +L KF  +S  F+KMR+++EKEGY 
Sbjct: 290  GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVRALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350  SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410  FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470  NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKI+KIAKEP+SME+P+ DD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590  TLAQKMDMPEDKIRKILKIAKEPISMETPISDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 650  DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 709

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FLEG+
Sbjct: 710  SRADKLKSFLEGQ 722



 Score =  827 bits (2136), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/598 (66%), Positives = 483/598 (80%), Gaps = 7/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 113 SPEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 172

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 173 QAPDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 232

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +
Sbjct: 233 EGEIEIAKRIEDGLKHMVMAISACPTTINEILAHITRVREGQAQIDEVVDGLVD---PED 289

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G     +E    +  +  +S++QLE L+  +L KF  +S  F+KMR+++EKEGY 
Sbjct: 290 GEEYAGAGVTADEDEADDGPAGGMSSKQLEDLRVRALAKFDEVSKQFEKMRQSYEKEGYK 349

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S++Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR H
Sbjct: 350 SDAYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSH 409

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K FP NE NL WV +E    H Y+  L R IP+++ELQQKLI+LQT +VLPL DL+D+
Sbjct: 410 FLKAFPGNETNLQWVLDEVAAAHAYSETLERQIPAVQELQQKLIDLQTRVVLPLKDLKDV 469

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 470 NKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 529

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 530 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 589

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKI+KIAKEP+SME+P+ DD+DSHLGDFIED   LAPSDAAL+ SMR
Sbjct: 590 TLAQKMDMPEDKIRKILKIAKEPISMETPISDDDDSHLGDFIEDTATLAPSDAALHGSMR 649

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 650 DVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 707


>gi|412338288|ref|YP_006967043.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica 253]
 gi|408768122|emb|CCJ52881.1| RNA polymerase sigma factor 70 [Bordetella bronchiseptica 253]
          Length = 722

 Score =  849 bits (2194), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/611 (66%), Positives = 496/611 (81%), Gaps = 7/611 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 115  EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 174

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 175  PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 234

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 235  EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 291

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
               G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY S+
Sbjct: 292  EYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYKSD 351

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            +Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR HF+
Sbjct: 352  AYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFL 411

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            K FP NE NL WV +E    H Y+  L R +P+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 412  KAFPGNETNLQWVLDEVAAAHAYSETLERQVPAVQELQQKLIDLQTRVVLPLKDLKDVNK 471

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 472  RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 531

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 532  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 591

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR V
Sbjct: 592  AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDV 651

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 652  VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 711

Query: 1420 YYKLKIFLEGK 1430
              KLK FLEG+
Sbjct: 712  ADKLKSFLEGQ 722



 Score =  827 bits (2135), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/596 (66%), Positives = 484/596 (81%), Gaps = 7/596 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +  
Sbjct: 115 EEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYDQA 174

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL++S      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR+G
Sbjct: 175 PDAETLLMSENAPVASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTREG 234

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D     +  
Sbjct: 235 EIEIAKRIEDGLKHMVMAISACPTTINEILAHILRVREGQAQIDEVVDGLVD---PEDGE 291

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
              G     +E    +  +  +S++QLE L+ ++L KF  +S  F+KMR+++EKEGY S+
Sbjct: 292 EYAGAGVTADEDEGDDGPAGGMSSKQLEDLRVKALAKFDEVSKQFEKMRQSYEKEGYKSD 351

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           +Y+KA + I  E++GIRFTAK +EKL DTLR Q+ +V Q+E+ +L   V++ GMPR HF+
Sbjct: 352 AYLKAQDIIQTELMGIRFTAKMVEKLADTLRAQVEEVRQLERAVLHTCVDRAGMPRSHFL 411

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           K FP NE NL WV +E    H Y+  L R +P+++ELQQKLI+LQT +VLPL DL+D+N+
Sbjct: 412 KAFPGNETNLQWVLDEVAAAHAYSETLERQVPAVQELQQKLIDLQTRVVLPLKDLKDVNK 471

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 472 RMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 531

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +
Sbjct: 532 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATL 591

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSDAAL+ SMR V
Sbjct: 592 AQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTATLAPSDAALHGSMRDV 651

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 652 VKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 707


>gi|300690868|ref|YP_003751863.1| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
 gi|299077928|emb|CBJ50567.2| RNA polymerase sigma70 factor [Ralstonia solanacearum PSI07]
          Length = 876

 Score =  847 bits (2187), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/634 (64%), Positives = 504/634 (79%), Gaps = 18/634 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 242  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 301

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 302  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 361

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 362  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 421

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL--------------STEQLEKLKYESLI 1035
            ID N  +          + E +        D               S  QLE+LK  +L+
Sbjct: 422  IDPNADAEAAAQAAADEDEEFEDEEAEEVGDEEEDEDDEGAGGAAASARQLEELKQAALV 481

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            +FS I   FDKMR+AFEKEGY S+ Y+KA  +I NE++ IRFTA+++E+LCDTLR Q+++
Sbjct: 482  RFSVIGDQFDKMRRAFEKEGYKSKPYLKAQESIQNELMAIRFTARTVERLCDTLRGQVDE 541

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+D+       Y+ I+ RNIP++ E
Sbjct: 542  VRKLERAILNIVVDKCGMPRGDFVSRFPGNETNLKWIDSVVADGKPYSAIVERNIPAVHE 601

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
            LQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGL
Sbjct: 602  LQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGL 661

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 662  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 721

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHL
Sbjct: 722  INKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHL 781

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQ
Sbjct: 782  GDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQ 841

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            FDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 842  FDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 875



 Score =  833 bits (2151), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/637 (63%), Positives = 502/637 (78%), Gaps = 18/637 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 225 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 284

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 285 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 344

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 345 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 404

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL----------- 231
           ++++ +E KIDE +DGLID N  +          + E +        D            
Sbjct: 405 ERVANDEAKIDEYIDGLIDPNADAEAAAQAAADEDEEFEDEEAEEVGDEEEDEDDEGAGG 464

Query: 232 ---STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
              S  QLE+LK  +L++FS I   FDKMR+AFEKEGY S+ Y+KA  +I NE++ IRFT
Sbjct: 465 AAASARQLEELKQAALVRFSVIGDQFDKMRRAFEKEGYKSKPYLKAQESIQNELMAIRFT 524

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+D+    
Sbjct: 525 ARTVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRGDFVSRFPGNETNLKWIDSVVAD 584

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEA
Sbjct: 585 GKPYSAIVERNIPAVHELQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEA 644

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 645 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 704

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 705 IADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAK 764

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 765 EPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMR 824

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 825 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 861


>gi|94311542|ref|YP_584752.1| RNA polymerase sigma factor RpoD [Cupriavidus metallidurans CH34]
 gi|93355394|gb|ABF09483.1| RNA polymerase sigma D factor (housekeeping sigma factor)
            [Cupriavidus metallidurans CH34]
          Length = 855

 Score =  846 bits (2186), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/634 (65%), Positives = 507/634 (79%), Gaps = 18/634 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   ++ S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T  
Sbjct: 221  FASSNQAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLN 280

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 281  DIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 340

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL +A++++  EIKIDE VDGL
Sbjct: 341  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVDGL 400

Query: 990  IDKNF-----SSNNRVIKGNKNNNEEKILIESSS---------ADLSTEQLEKLKYESLI 1035
            ID N      +S  + +  +  + +     +            A  S  QLE+LK  +L 
Sbjct: 401  IDPNAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESGGGAGASARQLEELKVAALE 460

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++
Sbjct: 461  KFRVIAEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMSIRFTARNVERLCDTLRGQVDE 520

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V ++E+ IL IVV+KCGMPR  F+  FP NE NL+W+         Y+ I+ RN+P++ E
Sbjct: 521  VRKLERAILNIVVDKCGMPRADFVARFPGNETNLDWIQTIVADNKSYSTIVERNVPAVHE 580

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
            LQQKLI+LQ+ +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGL
Sbjct: 581  LQQKLIDLQSRVVLPLKELKDVNRKMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGL 640

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 641  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 700

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHL
Sbjct: 701  INKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHL 760

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQ
Sbjct: 761  GDFIEDTNTLAPAEAALDGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQ 820

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            FDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 821  FDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 854



 Score =  833 bits (2151), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/647 (63%), Positives = 509/647 (78%), Gaps = 19/647 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   ++ S EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 202 TEKQKAKDRKAKEKALLKEFASSNQAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDH 261

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 262 LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 321

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 322 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 381

Query: 181 AADKISKNEIKIDEIVDGLIDKNF-----SSNNRVIKGNKNNNEEKILIESSS------- 228
           +A++++  EIKIDE VDGLID N      +S  + +  +  + +     +          
Sbjct: 382 SAERVANEEIKIDEFVDGLIDPNAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESG 441

Query: 229 --ADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
             A  S  QLE+LK  +L KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ IR
Sbjct: 442 GGAGASARQLEELKVAALEKFRVIAEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMSIR 501

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL+W+    
Sbjct: 502 FTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVARFPGNETNLDWIQTIV 561

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
                Y+ I+ RN+P++ ELQQKLI+LQ+ +VLPL +L+D+NRKM  GE +AR+AKREMT
Sbjct: 562 ADNKSYSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKDVNRKMSEGEKRAREAKREMT 621

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 622 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 681

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 682 RSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKI 741

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLR
Sbjct: 742 AKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALDGSMRDVVKDVLDSLTPREAKVLR 801

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 802 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKL 848


>gi|209517800|ref|ZP_03266635.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209501746|gb|EEA01767.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 680

 Score =  843 bits (2179), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 423/636 (66%), Positives = 514/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++ +E++IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANDEVRIDELV 223

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIE-------SSSADLSTEQLEKLKYES 1033
            DGLID +      FS+       N++   E+   E       S+ A  +  QLE L+  S
Sbjct: 224  DGLIDADAEDADGFSAQEAEAIENEDEEAEEEDEEDEEEDDGSAQATANAAQLEALRRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RNIP+I
Sbjct: 344  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVAEGHVYSAILTRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  830 bits (2144), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/639 (65%), Positives = 514/639 (80%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  TEKVKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIE-------S 226
             A++++ +E++IDE+VDGLID +      FS+       N++   E+   E       S
Sbjct: 207 AMAERVANDEVRIDELVDGLIDADAEDADGFSAQEAEAIENEDEEAEEEDEEDEEEDDGS 266

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE L+  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALRRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIV 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHVYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|307726543|ref|YP_003909756.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307587068|gb|ADN60465.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 803

 Score =  842 bits (2175), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/636 (66%), Positives = 512/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 168  KDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 226

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 227  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 286

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  E++IDE+V
Sbjct: 287  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEVRIDELV 346

Query: 987  DGLIDKN------FS-------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID +      FS        +    +  +   +E+    ++ A  +  Q+E LK  S
Sbjct: 347  DGLIDADAEDADGFSVQEAEAIESEDEEEEEEEEGDEEEDDGTAQATANAAQMEALKRAS 406

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 407  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQV 466

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RNIP+I
Sbjct: 467  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVSEGHSYSAILTRNIPAI 526

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 527  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 586

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 587  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 646

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 647  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 706

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 707  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 766

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 767  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 802



 Score =  827 bits (2136), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/638 (65%), Positives = 512/638 (80%), Gaps = 19/638 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K + ++++ KE  LLK+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 152 EKARARDRRAKEKALLKDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 210

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 211 LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 270

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 271 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 330

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FS-------SNNRVIKGNKNNNEEKILIESS 227
            A++++  E++IDE+VDGLID +      FS        +    +  +   +E+    ++
Sbjct: 331 MAERVANEEVRIDELVDGLIDADAEDADGFSVQEAEAIESEDEEEEEEEEGDEEEDDGTA 390

Query: 228 SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
            A  +  Q+E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRF
Sbjct: 391 QATANAAQMEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRF 450

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D    
Sbjct: 451 TARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVS 510

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
             H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTE
Sbjct: 511 EGHSYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTE 570

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 571 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 630

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 631 SIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIA 690

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRM
Sbjct: 691 KEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 750

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 751 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 788


>gi|295700835|ref|YP_003608728.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1002]
 gi|295440048|gb|ADG19217.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 680

 Score =  842 bits (2175), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 423/636 (66%), Positives = 513/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++ +E +IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANDENRIDELV 223

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIE-------SSSADLSTEQLEKLKYES 1033
            DGLID +      FS+       N++   E+   E       S+ A  +  QLE L+  S
Sbjct: 224  DGLIDADAEDADGFSAQEAEAIENEDEEAEEEDEEDEEEDDGSAQATANAAQLEALRRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RNIP+I
Sbjct: 344  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVAEGHAYSAILTRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  828 bits (2139), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/638 (65%), Positives = 513/638 (80%), Gaps = 19/638 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 29  EKVKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIE-------SS 227
            A++++ +E +IDE+VDGLID +      FS+       N++   E+   E       S+
Sbjct: 208 MAERVANDENRIDELVDGLIDADAEDADGFSAQEAEAIENEDEEAEEEDEEDEEEDDGSA 267

Query: 228 SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
            A  +  QLE L+  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRF
Sbjct: 268 QATANAAQLEALRRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRF 327

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D    
Sbjct: 328 TARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVA 387

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
             H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTE
Sbjct: 388 EGHAYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTE 447

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 448 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 507

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 508 SIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIA 567

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRM
Sbjct: 568 KEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 627

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|312795733|ref|YP_004028655.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
 gi|312167508|emb|CBW74511.1| RNA polymerase sigma factor rpoD [Burkholderia rhizoxinica HKI 454]
          Length = 778

 Score =  842 bits (2175), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/636 (65%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IESII 
Sbjct: 143  KEAFASH-QPGTAEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFAETEAIESIIS 201

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++    ++SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 202  TFNDMGVAVYEQAPDAETLLLNDNAPSVSSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 261

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++ +EI++DE+V
Sbjct: 262  REMGTVELLTREGEIEIAKRIEDGLKHMVQAISACPTTIADILAMAERVANDEIRVDELV 321

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTE-------------QLEKLKYES 1033
            DGLID N    +     + +  E +        +   E             QLE LK  S
Sbjct: 322  DGLIDPNAEDADGFSASDADEIESEADDADEGDEEEEEEDEGAGAAAASAAQLEALKRAS 381

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L +F+ I   FDKMR+A+EKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+
Sbjct: 382  LERFALIGEWFDKMRRAYEKEGYKSKSYLKAQEAIQAELMSIRFTARTVERLCDTLRAQV 441

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP NE NL+W +      H Y+ +L RNIP+I
Sbjct: 442  DEVRQVERQILHIVVDKCGMPRAEFIARFPSNETNLDWAEQIVAEGHPYSAVLERNIPAI 501

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+LI+LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 502  REQQQRLIDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 561

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 562  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 621

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 622  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 681

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 682  HLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 741

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 742  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 777



 Score =  828 bits (2140), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/639 (64%), Positives = 509/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 126 GEKIKARDRRAKEKALLKEAFASH-QPGTAEELEERRSKLRALIKLGKERGFLTYAEIND 184

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E IESII TF  M ++V E   D ETL+L++    ++SDD+VEE  E ALS
Sbjct: 185 HLPDNFAETEAIESIISTFNDMGVAVYEQAPDAETLLLNDNAPSVSSDDEVEEEAEVALS 244

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL
Sbjct: 245 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVQAISACPTTIADIL 304

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTE----- 234
             A++++ +EI++DE+VDGLID N    +     + +  E +        +   E     
Sbjct: 305 AMAERVANDEIRVDELVDGLIDPNAEDADGFSASDADEIESEADDADEGDEEEEEEDEGA 364

Query: 235 --------QLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                   QLE LK  SL +F+ I   FDKMR+A+EKEGY S+SY+KA   I  E++ IR
Sbjct: 365 GAAAASAAQLEALKRASLERFALIGEWFDKMRRAYEKEGYKSKSYLKAQEAIQAELMSIR 424

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE NL+W +   
Sbjct: 425 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRAEFIARFPSNETNLDWAEQIV 484

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ +L RNIP+I+E QQ+LI+LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 485 AEGHPYSAVLERNIPAIREQQQRLIDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 544

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 545 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 604

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 605 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 664

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 665 AKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 724

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 725 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 763


>gi|332284638|ref|YP_004416549.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
 gi|330428591|gb|AEC19925.1| RNA polymerase sigma factor RpoD [Pusillimonas sp. T7-7]
          Length = 749

 Score =  842 bits (2174), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/614 (65%), Positives = 496/614 (80%), Gaps = 14/614 (2%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE E  R + K+LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M ISV +  
Sbjct: 143  EEQEARRNRLKVLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYDQA 202

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D + L++S+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMG+VELLTR+G
Sbjct: 203  PDADALLMSDNAPVASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTREG 262

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSS 996
            EIEIAKRIE+GLK M+ AI++CPTT+ EIL    ++     +IDE+VDGLID+    ++ 
Sbjct: 263  EIEIAKRIEDGLKHMVMAIAACPTTVNEILQYIQRVRDGAAQIDEVVDGLIDQEGEEYAG 322

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
                +  ++N +         +  +S++QLE L+ +SL KF NIS  F KMR AFE++GY
Sbjct: 323  AGVSVDNDENED-------GPAGGMSSKQLEHLRTKSLKKFENISVWFSKMRTAFERDGY 375

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             ++ Y +A   I NE++G+RFTAK +EKL DTLR Q+ QV ++E+ +L   V++ GMPR 
Sbjct: 376  QAQEYAEAQEAILNELMGVRFTAKMVEKLADTLREQVAQVRKLERTVLHTCVDRAGMPRA 435

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FIKVFP NE NLNWV  E    H Y+  L R+IP+++E+QQKLI+LQT +VLPL DL+D
Sbjct: 436  YFIKVFPGNETNLNWVLEEVAAGHPYSETLERHIPAVQEIQQKLIDLQTSVVLPLKDLKD 495

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            +N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 496  VNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 555

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG+EPDP
Sbjct: 556  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGAEPDP 615

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
            + +A KM+MPE+K+RKI+KIAKEP+SME+P+GDD+DSHLGDFIED   L+PS+ AL+ SM
Sbjct: 616  ATLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDTGTLSPSEWALHGSM 675

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 676  RDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLRH 735

Query: 1417 PSRYYKLKIFLEGK 1430
            PSR  KLK FLEG+
Sbjct: 736  PSRADKLKSFLEGQ 749



 Score =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/632 (62%), Positives = 496/632 (78%), Gaps = 21/632 (3%)

Query: 1   MKFINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSE 60
           +K + K+   + K  K+   +N  +        EE E  R + K+LIKLGK+RGYLT+ E
Sbjct: 117 LKPLPKRGGKRGKADKDVPARNQMT-------PEEQEARRNRLKVLIKLGKDRGYLTYGE 169

Query: 61  INDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEA 116
           IND LP+D++D E I+ II TF  M ISV +   D + L++S+     +SDDDVE+  EA
Sbjct: 170 INDHLPDDLVDAEAIDGIISTFSDMGISVYDQAPDADALLMSDNAPVASSDDDVEDEAEA 229

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
           AL+TVDSDFGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AI++CPTT+ 
Sbjct: 230 ALTTVDSDFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAIAACPTTVN 289

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKGNKNNNEEKILIESSSADLST 233
           EIL    ++     +IDE+VDGLID+    ++     +  ++N +         +  +S+
Sbjct: 290 EILQYIQRVRDGAAQIDEVVDGLIDQEGEEYAGAGVSVDNDENED-------GPAGGMSS 342

Query: 234 EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIE 293
           +QLE L+ +SL KF NIS  F KMR AFE++GY ++ Y +A   I NE++G+RFTAK +E
Sbjct: 343 KQLEHLRTKSLKKFENISVWFSKMRTAFERDGYQAQEYAEAQEAILNELMGVRFTAKMVE 402

Query: 294 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 353
           KL DTLR Q+ QV ++E+ +L   V++ GMPR +FIKVFP NE NLNWV  E    H Y+
Sbjct: 403 KLADTLREQVAQVRKLERTVLHTCVDRAGMPRAYFIKVFPGNETNLNWVLEEVAAGHPYS 462

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
             L R+IP+++E+QQKLI+LQT +VLPL DL+D+N++M  GE KARKAKREMTEANLRLV
Sbjct: 463 ETLERHIPAVQEIQQKLIDLQTSVVLPLKDLKDVNKRMATGEAKARKAKREMTEANLRLV 522

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 523 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 582

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINK++RI+RQILQETG+EPDP+ +A KM+MPE+K+RKI+KIAKEP+SM
Sbjct: 583 RTIRIPVHMIETINKMNRINRQILQETGAEPDPATLAQKMDMPEDKVRKILKIAKEPISM 642

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GDD+DSHLGDFIED   L+PS+ AL+ SMR VVK++L+SLTPRE+KVLRMRFGIEM
Sbjct: 643 ETPIGDDDDSHLGDFIEDTGTLSPSEWALHGSMRDVVKEVLDSLTPREAKVLRMRFGIEM 702

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 703 STDQTLEEVGKQFDVTRERIRQIEAKALRKLR 734


>gi|420256203|ref|ZP_14759059.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
 gi|398043662|gb|EJL36548.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
          Length = 799

 Score =  840 bits (2170), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/636 (66%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 164  KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 222

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 223  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 282

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 283  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 342

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N    +                +   +  EE+    ++ A  +  QLE+LK  S
Sbjct: 343  DGLIDTNAEDTDGFSEQEAEAIENEEEEEAEADEEEEEDDDGAAQATANAAQLEELKRMS 402

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+
Sbjct: 403  LEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIRFTARTVERLCDTLRAQV 462

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RN+P+I
Sbjct: 463  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVTENHAYSAILSRNVPAI 522

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 523  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 582

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 583  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 642

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 643  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 702

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 703  HLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 762

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 763  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 798



 Score =  826 bits (2133), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/638 (65%), Positives = 509/638 (79%), Gaps = 19/638 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND 
Sbjct: 148 EKVKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEINDH 206

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALST
Sbjct: 207 LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALST 266

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 267 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 326

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESS 227
            A++++  EI+IDE+VDGLID N    +                +   +  EE+    ++
Sbjct: 327 MAERVANEEIRIDELVDGLIDTNAEDTDGFSEQEAEAIENEEEEEAEADEEEEEDDDGAA 386

Query: 228 SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
            A  +  QLE+LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRF
Sbjct: 387 QATANAAQLEELKRMSLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIRF 446

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D    
Sbjct: 447 TARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVT 506

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
             H Y+ IL RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTE
Sbjct: 507 ENHAYSAILSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTE 566

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 567 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 626

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 627 SIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIA 686

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRM
Sbjct: 687 KEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 746

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 747 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 784


>gi|319944403|ref|ZP_08018677.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
            ATCC 51599]
 gi|319742364|gb|EFV94777.1| DNA-directed RNA polymerase sigma subunit RpoD [Lautropia mirabilis
            ATCC 51599]
          Length = 785

 Score =  839 bits (2167), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/623 (64%), Positives = 504/623 (80%), Gaps = 5/623 (0%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K A +   +  + EE+E  R + + LIKLGKERG+LT++EIND LPE + + E I+ +I 
Sbjct: 165  KEALASVKQGVTEEEMEARRSRLRQLIKLGKERGFLTYAEINDHLPEGLTEVEAIDQMIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYMR 927
            TF  M ISV E   DT++L+L++ T   SDDD EE  EAALS+VDS+FGRT DP++MYMR
Sbjct: 225  TFSDMGISVYEQAPDTDSLLLNDRTVTSSDDDTEEEAEAALSSVDSEFGRTTDPVRMYMR 284

Query: 928  EMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD 987
            EMGSVELLTR+GEI IAK+IEEGLKDM+HAIS+CPTTI E+L  ADK+   ++++DEIVD
Sbjct: 285  EMGSVELLTREGEIVIAKKIEEGLKDMMHAISACPTTIAEVLEQADKVRAAQLRVDEIVD 344

Query: 988  GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
            GL+D +           +++ ++    E+S A ++  +LE+LK E+L +F +I   F++M
Sbjct: 345  GLLDPDADDEEMSFGPARSDGDDDD--EASVAAMNNAKLEELKEEALSRFDSIGAAFEQM 402

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            R+A E +GY S +Y+ A  ++  +++ IRFTAK +EKLCD LR Q+++V  +E+ IL+I 
Sbjct: 403  RQALETDGYKSPAYLAAQESVQRQLMSIRFTAKVVEKLCDMLRAQVDEVRTVERTILDIC 462

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            VN+ GM R HFIK FP NE NL WV+NE      Y  +L R+IP I++LQQKLI+LQ  +
Sbjct: 463  VNRVGMSREHFIKSFPGNETNLAWVENELAGNPPYADVLARSIPDIQDLQQKLIDLQVRV 522

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
            VLPL DL++IN++M  GEMKARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGN+G
Sbjct: 523  VLPLPDLKEINKRMAMGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVG 582

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQIL
Sbjct: 583  LMKAVDKFEFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQIL 642

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QETG EPDP+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAP
Sbjct: 643  QETGVEPDPATLAEKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTTTLAP 702

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            SDAAL+ SMR VVK++L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQIE
Sbjct: 703  SDAALHDSMREVVKEVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIE 762

Query: 1408 AKALRKLRHPSRYYKLKIFLEGK 1430
            AKALRKLRHPSR  KLK FLEG+
Sbjct: 763  AKALRKLRHPSRADKLKSFLEGQ 785



 Score =  822 bits (2124), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/623 (63%), Positives = 503/623 (80%), Gaps = 6/623 (0%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K + ++K++KE  L+K A +   +  + EE+E  R + + LIKLGKERG+LT++EIND L
Sbjct: 150 KGRGRDKRSKEKALIKEALASVKQGVTEEEMEARRSRLRQLIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT---SDDDVEEATEAALSTVD 122
           PE + + E I+ +I TF  M ISV E   DT++L+L++ T   SDDD EE  EAALS+VD
Sbjct: 210 PEGLTEVEAIDQMIGTFSDMGISVYEQAPDTDSLLLNDRTVTSSDDDTEEEAEAALSSVD 269

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMGSVELLTR+GEI IAK+IEEGLKDM+HAIS+CPTTI E+L  A
Sbjct: 270 SEFGRTTDPVRMYMREMGSVELLTREGEIVIAKKIEEGLKDMMHAISACPTTIAEVLEQA 329

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 242
           DK+   ++++DEIVDGL+D +           +++ ++    E+S A ++  +LE+LK E
Sbjct: 330 DKVRAAQLRVDEIVDGLLDPDADDEEMSFGPARSDGDDDD--EASVAAMNNAKLEELKEE 387

Query: 243 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 302
           +L +F +I   F++MR+A E +GY S +Y+ A  ++  +++ IRFTAK +EKLCD LR Q
Sbjct: 388 ALSRFDSIGAAFEQMRQALETDGYKSPAYLAAQESVQRQLMSIRFTAKVVEKLCDMLRAQ 447

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           +++V  +E+ IL+I VN+ GM R HFIK FP NE NL WV+NE      Y  +L R+IP 
Sbjct: 448 VDEVRTVERTILDICVNRVGMSREHFIKSFPGNETNLAWVENELAGNPPYADVLARSIPD 507

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I++LQQKLI+LQ  +VLPL DL++IN++M  GEMKARKAKREMTEANLRLVISIAKKYT+
Sbjct: 508 IQDLQQKLIDLQVRVVLPLPDLKEINKRMAMGEMKARKAKREMTEANLRLVISIAKKYTN 567

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGN+GLMKAVDKFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 568 RGLQFLDLIQEGNVGLMKAVDKFEFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHM 627

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQILQETG EPDP+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+D
Sbjct: 628 IETINKMNRISRQILQETGVEPDPATLAEKMDMPEDKIRKILKIAKEPISMETPIGDDDD 687

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED   LAPSDAAL+ SMR VVK++L+SLTPRE+KVLRMRFG+EMS+DHTLEEV
Sbjct: 688 SHLGDFIEDTTTLAPSDAALHDSMREVVKEVLDSLTPREAKVLRMRFGVEMSTDHTLEEV 747

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 748 GKQFDVTRERIRQIEAKALRKLR 770


>gi|238024932|ref|YP_002909164.1| RNA polymerase sigma factor RpoD [Burkholderia glumae BGR1]
 gi|237879597|gb|ACR31929.1| RNA polymerase sigma factor RpoD [Burkholderia glumae BGR1]
          Length = 805

 Score =  839 bits (2167), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/637 (65%), Positives = 510/637 (80%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 169  KEAFASS-QPGTAEELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 227

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 228  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 287

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++ +EI++DE+V
Sbjct: 288  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELV 347

Query: 987  DGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL+D N    +                 +    + EE+    ++ A  +  QLE LK  
Sbjct: 348  DGLLDPNAEDTDGFNAKEAEEAEEAEEEEEEANEDEEEEDDDGAAQATANAAQLEALKRA 407

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q
Sbjct: 408  SLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQ 467

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L W +      H Y+ IL RNIP+
Sbjct: 468  VDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLTWAEKVAAESHSYSAILVRNIPA 527

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 528  IHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 587

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 588  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 647

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 648  IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 707

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 708  SHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 767

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 768  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  826 bits (2133), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/639 (64%), Positives = 510/639 (79%), Gaps = 20/639 (3%)

Query: 6   KKTKIKNKKTKETLL-KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           K TK ++++ KE LL K AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 153 KTTKARDRRAKEKLLLKEAFASS-QPGTAEELEERRVKLRALIKLGKERGFLTYAEINDH 211

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 212 LPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 271

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL 
Sbjct: 272 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILA 331

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNN--------------RVIKGNKNNNEEKILIES 226
            A++++ +EI++DE+VDGL+D N    +                 +    + EE+    +
Sbjct: 332 MAERVANDEIRVDELVDGLLDPNAEDTDGFNAKEAEEAEEAEEEEEEANEDEEEEDDDGA 391

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 392 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 451

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L W +   
Sbjct: 452 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLTWAEKVA 511

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RNIP+I E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 512 AESHSYSAILVRNIPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 571

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 572 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 631

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 632 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 691

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 692 AKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 751

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 752 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|83716798|ref|YP_438821.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|83650623|gb|ABC34687.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 800

 Score =  838 bits (2165), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/636 (65%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 165  KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 223

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 224  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 283

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 284  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 343

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N +  +                    +  EE+    ++ A  +  QLE LK  S
Sbjct: 344  DGLIDPNAADTDGFSEKDAEEIENEDEEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 403

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 404  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 463

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 464  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 523

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 524  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 583

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 584  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 643

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 644  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 703

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 704  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 763

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 764  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 799



 Score =  825 bits (2130), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/639 (64%), Positives = 509/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 148 GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 206

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 207 HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 266

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 267 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 326

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIES 226
             A++++  EI++DE+VDGLID N +  +                    +  EE+    +
Sbjct: 327 AMAERVANEEIRVDELVDGLIDPNAADTDGFSEKDAEEIENEDEEAEEDDEEEEEDDDGA 386

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 387 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 446

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 447 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 506

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 507 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 566

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 567 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 626

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 627 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 686

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 687 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 746

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 747 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 785


>gi|393757579|ref|ZP_10346403.1| RNA polymerase sigma factor RpoD [Alcaligenes faecalis subsp.
            faecalis NCIB 8687]
 gi|393165271|gb|EJC65320.1| RNA polymerase sigma factor RpoD [Alcaligenes faecalis subsp.
            faecalis NCIB 8687]
          Length = 744

 Score =  838 bits (2165), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/675 (62%), Positives = 521/675 (77%), Gaps = 18/675 (2%)

Query: 763  AGRRA--ARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKNAFSFDIKS 820
             GRR   A+ A    + +  DD++ +   +PD   P   + K G K  +K     F ++ 
Sbjct: 81   GGRRGRPAKNANNDGIDFVDDDEMGEEEVIPD-LKP---VAKRGAK-RAKAEKDVFGVRG 135

Query: 821  N-SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 879
              S EE E  R + K LIKLGK+RGYLT+SEIND LP+D++D E I+ II TF  M ISV
Sbjct: 136  QLSPEEQEARRNRLKALIKLGKDRGYLTYSEINDHLPDDLVDVEAIDGIIGTFSDMGISV 195

Query: 880  SEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
             +   D +TL++S+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELL
Sbjct: 196  YDQAPDADTLLMSDNAPMASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELL 255

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+GEIEIAKRIE+GLK M+ AI++CPTT+ EIL    ++ +  ++IDE+VDGL+D +  
Sbjct: 256  TREGEIEIAKRIEDGLKHMVMAIAACPTTVNEILAYVQRVREGVMQIDEVVDGLVDDD-- 313

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
                   G   ++E+    E  +  +S++Q+E L+ +SL KF  I   FDKMR +FE EG
Sbjct: 314  GEEYAGSGVTADDED----EGPAGGMSSKQIEYLRNKSLKKFDIIGEWFDKMRVSFETEG 369

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y S  Y++A   I NE +GIRFTAK +EKL DT+R Q+  V Q E++IL I V++  MPR
Sbjct: 370  YKSPGYVQAQETILNEFMGIRFTAKMVEKLADTMREQVAIVRQHEREILTICVDRADMPR 429

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             HFIK FP NE NL+WV  E    H Y+ IL R+IP+I+E+QQKLI+LQT +VLPL DL+
Sbjct: 430  AHFIKAFPGNETNLDWVVQEVAAGHPYSAILERHIPAIQEIQQKLIDLQTSVVLPLKDLK 489

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            ++N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 490  EVNKRMTTGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 549

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG EPD
Sbjct: 550  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGVEPD 609

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P+ +A KM+MPE+K+RKI+KIAKEP+SME+P+GDD+DSHLGDFIED N ++PSD+AL+ S
Sbjct: 610  PATLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDNNTVSPSDSALHGS 669

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            MR VVKD+L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 670  MRDVVKDVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 729

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  KLK FLE +
Sbjct: 730  HPSRADKLKSFLESQ 744



 Score =  817 bits (2110), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 484/598 (80%), Gaps = 10/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+SEIND LP+D++D E I+ II TF  M ISV +
Sbjct: 138 SPEEQEARRNRLKALIKLGKDRGYLTYSEINDHLPDDLVDVEAIDGIIGTFSDMGISVYD 197

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D +TL++S+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 198 QAPDADTLLMSDNAPMASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 257

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AI++CPTT+ EIL    ++ +  ++IDE+VDGL+D +    
Sbjct: 258 EGEIEIAKRIEDGLKHMVMAIAACPTTVNEILAYVQRVREGVMQIDEVVDGLVDDD--GE 315

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G   ++E+    E  +  +S++Q+E L+ +SL KF  I   FDKMR +FE EGY 
Sbjct: 316 EYAGSGVTADDED----EGPAGGMSSKQIEYLRNKSLKKFDIIGEWFDKMRVSFETEGYK 371

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S  Y++A   I NE +GIRFTAK +EKL DT+R Q+  V Q E++IL I V++  MPR H
Sbjct: 372 SPGYVQAQETILNEFMGIRFTAKMVEKLADTMREQVAIVRQHEREILTICVDRADMPRAH 431

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIK FP NE NL+WV  E    H Y+ IL R+IP+I+E+QQKLI+LQT +VLPL DL+++
Sbjct: 432 FIKAFPGNETNLDWVVQEVAAGHPYSAILERHIPAIQEIQQKLIDLQTSVVLPLKDLKEV 491

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 492 NKRMTTGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 551

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG EPDP+
Sbjct: 552 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGVEPDPA 611

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+K+RKI+KIAKEP+SME+P+GDD+DSHLGDFIED N ++PSD+AL+ SMR
Sbjct: 612 TLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDNNTVSPSDSALHGSMR 671

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVKD+L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 672 DVVKDVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 729


>gi|430809195|ref|ZP_19436310.1| RNA polymerase sigma factor RpoD [Cupriavidus sp. HMR-1]
 gi|429498339|gb|EKZ96849.1| RNA polymerase sigma factor RpoD [Cupriavidus sp. HMR-1]
          Length = 752

 Score =  837 bits (2163), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/634 (65%), Positives = 507/634 (79%), Gaps = 18/634 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   ++ S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T  
Sbjct: 118  FASSNQAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLN 177

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 178  DIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 237

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL +A++++  EIKIDE VDGL
Sbjct: 238  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILASAERVANEEIKIDEFVDGL 297

Query: 990  IDKNF-----SSNNRVIKGNKNNNEEKILIESSS---------ADLSTEQLEKLKYESLI 1035
            ID N      +S  + +  +  + +     +            A  S  QLE+LK  +L 
Sbjct: 298  IDPNAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESGGGAGASARQLEELKVAALE 357

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++
Sbjct: 358  KFRVIAEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMSIRFTARNVERLCDTLRGQVDE 417

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V ++E+ IL IVV+KCGMPR  F+  FP NE NL+W+         Y+ I+ RN+P++ E
Sbjct: 418  VRKLERAILNIVVDKCGMPRADFVARFPGNETNLDWIQTIVADGKSYSTIVERNVPAVHE 477

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
            LQQKLI+LQ+ +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGL
Sbjct: 478  LQQKLIDLQSRVVLPLKELKDVNRKMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGL 537

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 538  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 597

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHL
Sbjct: 598  INKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHL 657

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQ
Sbjct: 658  GDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQ 717

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            FDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 718  FDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 751



 Score =  825 bits (2131), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/639 (64%), Positives = 506/639 (79%), Gaps = 18/639 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   ++ S EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 99  TEKQKAKDRKAKEKALLKEFASSNQAGSEEELEIRRQKLKALIKLGKSRGYLTYAEINDH 158

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 159 LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 218

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 219 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 278

Query: 181 AADKISKNEIKIDEIVDGLIDKNF-----SSNNRVIKGNKNNNEEKILIESSS------- 228
           +A++++  EIKIDE VDGLID N      +S  + +  +  + +     +          
Sbjct: 279 SAERVANEEIKIDEFVDGLIDPNAEEVQDNSPAQAVAADDEDEDSDEDGDDGEEEDDESG 338

Query: 229 --ADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
             A  S  QLE+LK  +L KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ IR
Sbjct: 339 GGAGASARQLEELKVAALEKFRVIAEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMSIR 398

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL+W+    
Sbjct: 399 FTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVARFPGNETNLDWIQTIV 458

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
                Y+ I+ RN+P++ ELQQKLI+LQ+ +VLPL +L+D+NRKM  GE +AR+AKREMT
Sbjct: 459 ADGKSYSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKDVNRKMSEGEKRAREAKREMT 518

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 519 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 578

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 579 RSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKI 638

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLR
Sbjct: 639 AKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLR 698

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 699 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 737


>gi|76817579|ref|YP_335991.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
 gi|76582052|gb|ABA51526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710b]
          Length = 800

 Score =  837 bits (2163), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/636 (65%), Positives = 505/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 165  KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 223

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 224  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 283

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 284  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 343

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 344  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 403

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 404  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 463

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 464  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 523

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 524  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 583

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 584  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 643

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 644  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 703

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 704  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 763

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 764  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 799



 Score =  823 bits (2127), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/639 (64%), Positives = 505/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 148 GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 206

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 207 HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 266

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 267 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 326

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 327 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 386

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 387 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 446

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 447 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 506

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 507 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 566

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 567 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 626

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 627 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 686

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 687 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 746

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 747 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 785


>gi|424776087|ref|ZP_18203072.1| RNA polymerase sigma factor RpoD [Alcaligenes sp. HPC1271]
 gi|422888547|gb|EKU30933.1| RNA polymerase sigma factor RpoD [Alcaligenes sp. HPC1271]
          Length = 721

 Score =  837 bits (2162), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/675 (62%), Positives = 521/675 (77%), Gaps = 18/675 (2%)

Query: 763  AGRRA--ARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKNAFSFDIKS 820
             GRR   A+ A    + +  DD++ +   +PD   P   + K G K  +K     F ++ 
Sbjct: 58   GGRRGRPAKNANNDGIDFVDDDEMGEEEVIPD-LKP---VAKRGAK-RAKAEKDVFGVRG 112

Query: 821  N-SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 879
              S EE E  R + K LIKLGK+RGYLT+SEIND LP+D++D E I+ II TF  M ISV
Sbjct: 113  QLSPEEQEARRNRLKALIKLGKDRGYLTYSEINDHLPDDLVDVEAIDGIIGTFSDMGISV 172

Query: 880  SEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
             +   D +TL++S+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELL
Sbjct: 173  YDQAPDADTLLMSDNAPMASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELL 232

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+GEIEIAKRIE+GLK M+ AI++CPTT+ EIL    ++ +  ++IDE+VDGL+D +  
Sbjct: 233  TREGEIEIAKRIEDGLKHMVMAIAACPTTVNEILAYVQRVREGVMQIDEVVDGLVDDD-- 290

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
                   G   ++E+    E  +  +S++Q+E L+ +SL KF  I   FDKMR +FE EG
Sbjct: 291  GEEYAGSGVTADDED----EGPAGGMSSKQIEYLRNKSLKKFDIIGEWFDKMRVSFESEG 346

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y S  Y++A   I NE +GIRFTAK +EKL DT+R Q+  V Q E++IL I V++  MPR
Sbjct: 347  YKSAGYVQAQETILNEFMGIRFTAKMVEKLADTMREQVAIVRQHEREILNICVDRADMPR 406

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             HFIK FP NE NL+WV  E    H Y+ IL R+IP+I+E+QQKLI+LQT +VLPL DL+
Sbjct: 407  AHFIKAFPGNETNLDWVVQEVAAGHPYSSILERHIPAIQEVQQKLIDLQTSVVLPLKDLK 466

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            ++N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 467  EVNKRMTTGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 526

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG EPD
Sbjct: 527  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGVEPD 586

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P+ +A KM+MPE+K+RKI+KIAKEP+SME+P+GDD+DSHLGDFIED N ++PSD+AL+ S
Sbjct: 587  PATLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDNNTVSPSDSALHGS 646

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            MR VVKD+L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 647  MRDVVKDVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 706

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  KLK FLE +
Sbjct: 707  HPSRADKLKSFLESQ 721



 Score =  816 bits (2108), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/598 (66%), Positives = 484/598 (80%), Gaps = 10/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+SEIND LP+D++D E I+ II TF  M ISV +
Sbjct: 115 SPEEQEARRNRLKALIKLGKDRGYLTYSEINDHLPDDLVDVEAIDGIIGTFSDMGISVYD 174

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D +TL++S+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMGSVELLTR
Sbjct: 175 QAPDADTLLMSDNAPMASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELLTR 234

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK M+ AI++CPTT+ EIL    ++ +  ++IDE+VDGL+D +    
Sbjct: 235 EGEIEIAKRIEDGLKHMVMAIAACPTTVNEILAYVQRVREGVMQIDEVVDGLVDDD--GE 292

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                G   ++E+    E  +  +S++Q+E L+ +SL KF  I   FDKMR +FE EGY 
Sbjct: 293 EYAGSGVTADDED----EGPAGGMSSKQIEYLRNKSLKKFDIIGEWFDKMRVSFESEGYK 348

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S  Y++A   I NE +GIRFTAK +EKL DT+R Q+  V Q E++IL I V++  MPR H
Sbjct: 349 SAGYVQAQETILNEFMGIRFTAKMVEKLADTMREQVAIVRQHEREILNICVDRADMPRAH 408

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIK FP NE NL+WV  E    H Y+ IL R+IP+I+E+QQKLI+LQT +VLPL DL+++
Sbjct: 409 FIKAFPGNETNLDWVVQEVAAGHPYSSILERHIPAIQEVQQKLIDLQTSVVLPLKDLKEV 468

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 469 NKRMTTGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 528

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG EPDP+
Sbjct: 529 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGVEPDPA 588

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+K+RKI+KIAKEP+SME+P+GDD+DSHLGDFIED N ++PSD+AL+ SMR
Sbjct: 589 TLAQKMDMPEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDNNTVSPSDSALHGSMR 648

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            VVKD+L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 649 DVVKDVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 706


>gi|115358008|ref|YP_775146.1| RNA polymerase sigma factor RpoD [Burkholderia ambifaria AMMD]
 gi|115283296|gb|ABI88812.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria AMMD]
          Length = 805

 Score =  837 bits (2162), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/640 (65%), Positives = 512/640 (80%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 345  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 404

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 405  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQTELMTIRFTARTVERLCDTL 464

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 465  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKITAEGHSYSAVLARN 524

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 525  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 584

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 585  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 644

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 645  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 704

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 705  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 764

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  825 bits (2130), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/641 (64%), Positives = 513/641 (80%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 330 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 389

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I  E++ 
Sbjct: 390 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQTELMT 449

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 450 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 509

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 510 ITAEGHSYSAVLARNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 569

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 570 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 629

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 630 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 689

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 690 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 749

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|386332883|ref|YP_006029052.1| RNA polymerase sigma70 factor [Ralstonia solanacearum Po82]
 gi|334195331|gb|AEG68516.1| RNA polymerase sigma70 factor [Ralstonia solanacearum Po82]
          Length = 873

 Score =  837 bits (2161), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/631 (64%), Positives = 505/631 (80%), Gaps = 15/631 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 242  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 301

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 302  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 361

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 362  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 421

Query: 990  IDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            ID N  +  +                 +  E++    +  A  S  QLE+LK  +L KFS
Sbjct: 422  IDLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAASARQLEELKQAALEKFS 481

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V +
Sbjct: 482  IIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRK 541

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQ
Sbjct: 542  LERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQ 601

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFL
Sbjct: 602  KLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFL 661

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 662  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 721

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 722  MNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDF 781

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDV
Sbjct: 782  IEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDV 841

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            TRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 842  TRERIRQIEAKALRKLRHPSRSDKLKSFLEG 872



 Score =  822 bits (2124), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/634 (63%), Positives = 503/634 (79%), Gaps = 15/634 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 225 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 284

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 285 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 344

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 345 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 404

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADL 231
           ++++ +E KIDE +DGLID N  +  +                 +  E++    +  A  
Sbjct: 405 ERVANDEAKIDEYIDGLIDLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAA 464

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           S  QLE+LK  +L KFS I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA++
Sbjct: 465 SARQLEELKQAALEKFSIIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARN 524

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++        
Sbjct: 525 VERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP 584

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ I+ RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLR
Sbjct: 585 YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLR 644

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 645 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 704

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+
Sbjct: 705 QARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPI 764

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGI
Sbjct: 765 SMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGI 824

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 825 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 858


>gi|91777317|ref|YP_552525.1| RNA polymerase sigma factor RpoD [Burkholderia xenovorans LB400]
 gi|91689977|gb|ABE33175.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
            LB400]
          Length = 680

 Score =  837 bits (2161), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/640 (65%), Positives = 508/640 (79%), Gaps = 26/640 (4%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-----------------LEKL 1029
            DGLID N    +    G      E I  E    +  +E+                 +E L
Sbjct: 224  DGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDSEEDEEEDDGTAQATANAAQMEAL 279

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTL
Sbjct: 280  KRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTL 339

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RN
Sbjct: 340  RAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVGEGHAYSAILTRN 399

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 400  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 459

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 460  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 519

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 520  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 579

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 580  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 639

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 640  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  823 bits (2125), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/642 (64%), Positives = 508/642 (79%), Gaps = 27/642 (4%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 29  EKAKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ----- 235
            A++++  EI+IDE+VDGLID N    +    G      E I  E    +  +E+     
Sbjct: 208 MAERVANEEIRIDELVDGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDSEEDEEED 263

Query: 236 ------------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
                       +E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++
Sbjct: 264 DGTAQATANAAQMEALKRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELM 323

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
            IRFTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D
Sbjct: 324 TIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWAD 383

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
                 H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKR
Sbjct: 384 KIVGEGHAYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKR 443

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 444 EMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 503

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKI
Sbjct: 504 AITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKI 563

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           MKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+K
Sbjct: 564 MKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAK 623

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 624 VLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|385206466|ref|ZP_10033336.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
 gi|385186357|gb|EIF35631.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
          Length = 680

 Score =  837 bits (2161), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/640 (65%), Positives = 507/640 (79%), Gaps = 26/640 (4%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-----------------LEKL 1029
            DGLID N    +    G      E I  E    +   E+                 +E L
Sbjct: 224  DGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDAEEDEEEDDGTAQATANAAQMEAL 279

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTL
Sbjct: 280  KRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTL 339

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RN
Sbjct: 340  RAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVGEGHAYSAILTRN 399

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 400  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 459

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 460  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 519

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 520  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 579

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 580  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 639

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 640  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  823 bits (2125), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/642 (64%), Positives = 507/642 (78%), Gaps = 27/642 (4%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 29  EKAKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ----- 235
            A++++  EI+IDE+VDGLID N    +    G      E I  E    +   E+     
Sbjct: 208 MAERVANEEIRIDELVDGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDAEEDEEED 263

Query: 236 ------------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
                       +E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++
Sbjct: 264 DGTAQATANAAQMEALKRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELM 323

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
            IRFTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D
Sbjct: 324 TIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWAD 383

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
                 H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKR
Sbjct: 384 KIVGEGHAYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKR 443

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 444 EMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 503

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKI
Sbjct: 504 AITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKI 563

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           MKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+K
Sbjct: 564 MKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAK 623

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 624 VLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|323529251|ref|YP_004231403.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386253|gb|ADX58343.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 680

 Score =  836 bits (2160), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 423/642 (65%), Positives = 508/642 (79%), Gaps = 30/642 (4%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------------LE 1027
            DGLID +          +  + +E   IES   D   E                    +E
Sbjct: 224  DGLIDADAED------ADGFSVQEAEAIESEDEDEEEEDEEDEEEDDGTAQATANAAQME 277

Query: 1028 KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 1087
             LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCD
Sbjct: 278  ALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCD 337

Query: 1088 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILC 1147
            TLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL 
Sbjct: 338  TLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVAEGHSYSAILT 397

Query: 1148 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 1207
            RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIA
Sbjct: 398  RNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIA 457

Query: 1208 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 1267
            KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR
Sbjct: 458  KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 517

Query: 1268 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327
            IPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+
Sbjct: 518  IPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPI 577

Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387
            GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DH
Sbjct: 578  GDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDH 637

Query: 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 638  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/644 (64%), Positives = 508/644 (78%), Gaps = 31/644 (4%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K + ++++ KE  LLK+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 29  EKARARDRRAKEKALLKDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ----- 235
            A++++  EI+IDE+VDGLID +          +  + +E   IES   D   E      
Sbjct: 208 MAERVANEEIRIDELVDGLIDADAED------ADGFSVQEAEAIESEDEDEEEEDEEDEE 261

Query: 236 --------------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 281
                         +E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE
Sbjct: 262 EDDGTAQATANAAQMEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNE 321

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           ++ IRFTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W
Sbjct: 322 LMTIRFTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEW 381

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
            D      H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+A
Sbjct: 382 ADKIVAEGHSYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQA 441

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           KREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 442 KREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 501

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIR
Sbjct: 502 RQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIR 561

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           KIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE
Sbjct: 562 KIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPRE 621

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 622 AKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|300703499|ref|YP_003745101.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
 gi|299071162|emb|CBJ42476.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CFBP2957]
          Length = 873

 Score =  836 bits (2160), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/631 (64%), Positives = 503/631 (79%), Gaps = 15/631 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 242  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 301

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 302  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 361

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 362  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 421

Query: 990  IDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            ID N  +  +                    E++    +  +  S  QLE+LK  +L KFS
Sbjct: 422  IDPNAEAEAQSADEDEDFEDEEADEGDEEEEDEDDDGAGGSAASARQLEELKQAALEKFS 481

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA+++E+LCDTLR Q+++V +
Sbjct: 482  IIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRK 541

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQ
Sbjct: 542  LERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQ 601

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFL
Sbjct: 602  KLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFL 661

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 662  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 721

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 722  MNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDF 781

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDV
Sbjct: 782  IEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDV 841

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            TRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 842  TRERIRQIEAKALRKLRHPSRSDKLKSFLEG 872



 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/634 (63%), Positives = 501/634 (79%), Gaps = 15/634 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 225 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 284

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 285 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 344

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 345 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 404

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADL 231
           ++++ +E KIDE +DGLID N  +  +                    E++    +  +  
Sbjct: 405 ERVANDEAKIDEYIDGLIDPNAEAEAQSADEDEDFEDEEADEGDEEEEDEDDDGAGGSAA 464

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           S  QLE+LK  +L KFS I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA++
Sbjct: 465 SARQLEELKQAALEKFSIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARN 524

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++        
Sbjct: 525 VERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP 584

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ I+ RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLR
Sbjct: 585 YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLR 644

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 645 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 704

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+
Sbjct: 705 QARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPI 764

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGI
Sbjct: 765 SMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGI 824

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 825 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 858


>gi|161521349|ref|YP_001584776.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
            17616]
 gi|189352484|ref|YP_001948111.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
            17616]
 gi|160345399|gb|ABX18484.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia multivorans ATCC
            17616]
 gi|189336506|dbj|BAG45575.1| RNA polymerase primary sigma factor [Burkholderia multivorans ATCC
            17616]
          Length = 804

 Score =  836 bits (2160), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/639 (65%), Positives = 513/639 (80%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++ +EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELV 344

Query: 987  DGLIDKNFSSNN----------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N S  +                  ++  +   EE+    ++ A  +  QLE LK
Sbjct: 345  DGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEALK 404

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
              SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ IRFTA+++E+LCDTLR
Sbjct: 405  RASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTIRFTARTVERLCDTLR 464

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +      H Y+ IL RNI
Sbjct: 465  AQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKIAAEGHSYSAILSRNI 524

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKY
Sbjct: 525  PAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKY 584

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 585  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 644

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 645  HMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDD 704

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 705  DDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 764

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 803



 Score =  824 bits (2128), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/640 (64%), Positives = 514/640 (80%), Gaps = 22/640 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNN----------------RVIKGNKNNNEEKILIE 225
           A++++ +EI++DE+VDGL+D N S  +                  ++  +   EE+    
Sbjct: 330 AERVANDEIRVDELVDGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDG 389

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++ A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ I
Sbjct: 390 AAQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTI 449

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +  
Sbjct: 450 RFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKI 509

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
               H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREM
Sbjct: 510 AAEGHSYSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREM 569

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 570 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 629

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 630 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMK 689

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVL
Sbjct: 690 IAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 749

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 789


>gi|167577173|ref|ZP_02370047.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
 gi|167615343|ref|ZP_02383978.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
          Length = 680

 Score =  836 bits (2160), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/636 (65%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 45   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 223

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N +  +                    +  EE+    ++ A  +  QLE LK  S
Sbjct: 224  DGLIDPNAADTDGFSEKDAEEIENEDEEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 344  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  823 bits (2125), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/639 (64%), Positives = 509/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIES 226
             A++++  EI++DE+VDGLID N +  +                    +  EE+    +
Sbjct: 207 AMAERVANEEIRVDELVDGLIDPNAADTDGFSEKDAEEIENEDEEAEEDDEEEEEDDDGA 266

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|116691983|ref|YP_837516.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia HI2424]
 gi|116649983|gb|ABK10623.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
            HI2424]
          Length = 805

 Score =  836 bits (2159), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/640 (65%), Positives = 513/640 (80%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 345  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 404

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTL
Sbjct: 405  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTL 464

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 465  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKITAEGHPYSAVLSRN 524

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 525  VPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 584

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 585  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 644

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 645  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 704

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 705  DDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 764

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  824 bits (2128), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/641 (64%), Positives = 514/641 (80%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 330 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 389

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ 
Sbjct: 390 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMT 449

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 450 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 509

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 510 ITAEGHPYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 569

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 570 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 629

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 630 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 689

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 690 KIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKV 749

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|172062815|ref|YP_001810466.1| RNA polymerase sigma factor RpoD [Burkholderia ambifaria MC40-6]
 gi|171995332|gb|ACB66250.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
            MC40-6]
          Length = 805

 Score =  836 bits (2159), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/640 (65%), Positives = 511/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 345  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEAL 404

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 405  KRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTL 464

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RN
Sbjct: 465  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRN 524

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 525  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 584

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 585  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 644

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 645  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 704

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 705  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 764

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  824 bits (2128), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/641 (64%), Positives = 512/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 330 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDD 389

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ 
Sbjct: 390 GAAQATANAAQLEALKRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMT 449

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 450 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 509

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
                H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 510 IAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 569

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 570 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 629

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 630 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 689

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 690 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 749

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|407710092|ref|YP_006793956.1| RNA polymerase primary sigma factor [Burkholderia phenoliruptrix
            BR3459a]
 gi|407238775|gb|AFT88973.1| RNA polymerase primary sigma factor [Burkholderia phenoliruptrix
            BR3459a]
          Length = 680

 Score =  835 bits (2158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 425/636 (66%), Positives = 511/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 45   KDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 223

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------LEKLKYES 1033
            DGLID +      FS        +++  EE+   E    D  T Q       +E LK  S
Sbjct: 224  DGLIDADAEDADGFSVQEAEAIESEDEEEEEEDEEDEEEDDGTAQATANAAQMEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RNIP+I
Sbjct: 344  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVAEGHSYSAILTRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  821 bits (2120), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/638 (65%), Positives = 511/638 (80%), Gaps = 19/638 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K + ++++ KE  LLK+AFS   +  + EE+E  R K + LIKLGKERG+LT++EIND 
Sbjct: 29  EKARARDRRAKEKALLKDAFSSS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLSTE 234
            A++++  EI+IDE+VDGLID +      FS        +++  EE+   E    D  T 
Sbjct: 208 MAERVANEEIRIDELVDGLIDADAEDADGFSVQEAEAIESEDEEEEEEDEEDEEEDDGTA 267

Query: 235 Q-------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
           Q       +E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRF
Sbjct: 268 QATANAAQMEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRF 327

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D    
Sbjct: 328 TARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVA 387

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
             H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTE
Sbjct: 388 EGHSYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTE 447

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 448 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 507

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 508 SIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIA 567

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRM
Sbjct: 568 KEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 627

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|187921407|ref|YP_001890439.1| RNA polymerase sigma factor RpoD [Burkholderia phytofirmans PsJN]
 gi|187719845|gb|ACD21068.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
            PsJN]
          Length = 681

 Score =  835 bits (2158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/640 (65%), Positives = 508/640 (79%), Gaps = 26/640 (4%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E IE II 
Sbjct: 46   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNFTETEAIEGIIS 104

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 105  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 164

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 165  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 224

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-----------------LEKL 1029
            DGLID N    +    G      E I  E    +  +E+                 +E L
Sbjct: 225  DGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDSEEDEEEDDGTAQATANAAQMEAL 280

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTL
Sbjct: 281  KRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFTARTVERLCDTL 340

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RN
Sbjct: 341  RAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVGEGHAYSAILTRN 400

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 401  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 460

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 461  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 520

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 521  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 580

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 581  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 640

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 641  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score =  819 bits (2115), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/637 (65%), Positives = 505/637 (79%), Gaps = 27/637 (4%)

Query: 11  KNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDI 69
           ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT++EIND LP++ 
Sbjct: 35  RDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYAEINDHLPDNF 93

Query: 70  IDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDF 125
            + E IE II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+F
Sbjct: 94  TETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEF 153

Query: 126 GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 185
           GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A+++
Sbjct: 154 GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERV 213

Query: 186 SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---------- 235
           +  EI+IDE+VDGLID N    +    G      E I  E    +  +E+          
Sbjct: 214 ANEEIRIDELVDGLIDANAEDAD----GFSAQEAEAIESEDEEVEEDSEEDEEEDDGTAQ 269

Query: 236 -------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
                  +E LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFT
Sbjct: 270 ATANAAQMEALKRASLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMTIRFT 329

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D     
Sbjct: 330 ARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVGE 389

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
            H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEA
Sbjct: 390 GHAYSAILTRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEA 449

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 450 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 509

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 510 IADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAK 569

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 570 EPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMR 629

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 630 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|187929499|ref|YP_001899986.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12J]
 gi|404396614|ref|ZP_10988408.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_2_56FAA]
 gi|187726389|gb|ACD27554.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12J]
 gi|348613704|gb|EGY63283.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_2_56FAA]
          Length = 829

 Score =  835 bits (2158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/632 (64%), Positives = 502/632 (79%), Gaps = 16/632 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +E+++ T  
Sbjct: 197  FAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLN 256

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 257  DIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 316

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 317  GTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 376

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL------------STEQLEKLKYESLIKF 1037
            ID N  ++       +   EE+   E    +             S  QLE+LK  +L+KF
Sbjct: 377  IDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAASARQLEELKQAALLKF 436

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++V 
Sbjct: 437  GVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVR 496

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            ++E+ IL IVV+KCGMPR  F+  FP NE NL W++        Y+ I+ RN+P++ ELQ
Sbjct: 497  KLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVADGKPYSTIVERNVPAVHELQ 556

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQF
Sbjct: 557  QKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQF 616

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 617  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 676

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 677  KMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 736

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFD
Sbjct: 737  FIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFD 796

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 797  VTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 828



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/637 (63%), Positives = 501/637 (78%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 178 TEKLKARDRKAKEKALLKEFAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDH 237

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E +E+++ T   + ++V E   D ETL+L++    +T++++ EE  EAALST
Sbjct: 238 LPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALST 297

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 298 VDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILA 357

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL--------- 231
             ++++ +E KIDE +DGLID N  ++       +   EE+   E    +          
Sbjct: 358 MGERVANDEAKIDEYIDGLIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGA 417

Query: 232 ---STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
              S  QLE+LK  +L+KF  I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFT
Sbjct: 418 AAASARQLEELKQAALLKFGVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFT 477

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W++     
Sbjct: 478 ARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVAD 537

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ I+ RN+P++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEA
Sbjct: 538 GKPYSTIVERNVPAVHELQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEA 597

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 598 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 657

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 658 IADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAK 717

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 718 EPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMR 777

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 778 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 814


>gi|121597172|ref|YP_991115.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126456327|ref|YP_001076416.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|121224970|gb|ABM48501.1| RNA polymerase sigma factor RpoD [Burkholderia mallei SAVP1]
 gi|126230095|gb|ABN93508.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
          Length = 736

 Score =  835 bits (2158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/636 (65%), Positives = 505/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 101  KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 159

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 160  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 219

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 220  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 279

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 280  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 339

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 340  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 399

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 400  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 459

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 460  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 519

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 520  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 579

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 580  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 639

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 640  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 699

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 700  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 735



 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/639 (64%), Positives = 505/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 84  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 142

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 143 HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 202

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 203 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 262

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 263 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 322

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 323 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 382

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 383 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 442

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 443 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 502

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 503 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 562

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 563 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 622

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 623 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 682

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 683 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 721


>gi|241663618|ref|YP_002981978.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12D]
 gi|240865645|gb|ACS63306.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12D]
          Length = 821

 Score =  835 bits (2158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/632 (64%), Positives = 502/632 (79%), Gaps = 16/632 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +E+++ T  
Sbjct: 189  FAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLN 248

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 249  DIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 308

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 309  GTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 368

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL------------STEQLEKLKYESLIKF 1037
            ID N  ++       +   EE+   E    +             S  QLE+LK  +L+KF
Sbjct: 369  IDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAASARQLEELKQAALVKF 428

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++V 
Sbjct: 429  GVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVR 488

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            ++E+ IL IVV+KCGMPR  F+  FP NE NL W++        Y+ I+ RN+P++ ELQ
Sbjct: 489  KLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVADGKPYSTIVERNVPAVHELQ 548

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQF
Sbjct: 549  QKLIDLQARVVLPLAELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQF 608

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 609  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 668

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 669  KMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 728

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFD
Sbjct: 729  FIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFD 788

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 789  VTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 820



 Score =  821 bits (2120), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/637 (63%), Positives = 501/637 (78%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 170 TEKLKARDRKAKEKALLKEFAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDH 229

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E +E+++ T   + ++V E   D ETL+L++    +T++++ EE  EAALST
Sbjct: 230 LPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALST 289

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 290 VDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILA 349

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL--------- 231
             ++++ +E KIDE +DGLID N  ++       +   EE+   E    +          
Sbjct: 350 MGERVANDEAKIDEYIDGLIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGA 409

Query: 232 ---STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
              S  QLE+LK  +L+KF  I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFT
Sbjct: 410 AAASARQLEELKQAALVKFGVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFT 469

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W++     
Sbjct: 470 ARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVAD 529

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ I+ RN+P++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEA
Sbjct: 530 GKPYSTIVERNVPAVHELQQKLIDLQARVVLPLAELKDVNRKMSEGERRAREAKREMTEA 589

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 590 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 649

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 650 IADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAK 709

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 710 EPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMR 769

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 770 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806


>gi|344171945|emb|CCA84571.1| RNA polymerase sigma70 factor [Ralstonia syzygii R24]
          Length = 699

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/634 (64%), Positives = 504/634 (79%), Gaps = 18/634 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 65   FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 124

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 125  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 184

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 185  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 244

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL--------------STEQLEKLKYESLI 1035
            ID N  +          + E +        D               S  QLE+LK  +L+
Sbjct: 245  IDPNADAEAAAQAAADEDEEFEDEEAEEVGDEEEDEDDEGAGGAAASARQLEELKQAALV 304

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            +FS I   FDKMR+AFEKEGY S+ Y+KA  +I NE++ IRFTA+++E+LCDTLR Q+++
Sbjct: 305  RFSVIGDQFDKMRRAFEKEGYKSKPYLKAQESIQNELMAIRFTARTVERLCDTLRGQVDE 364

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+D+       Y+ I+ RNIP++ E
Sbjct: 365  VRKLERAILNIVVDKCGMPRGDFVSRFPGNETNLRWIDSVVADGKPYSAIVERNIPAVHE 424

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
            LQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGL
Sbjct: 425  LQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGL 484

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 485  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 544

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHL
Sbjct: 545  INKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHL 604

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQ
Sbjct: 605  GDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQ 664

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            FDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 665  FDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 698



 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/637 (63%), Positives = 502/637 (78%), Gaps = 18/637 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 48  KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 107

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 108 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 167

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 168 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 227

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL----------- 231
           ++++ +E KIDE +DGLID N  +          + E +        D            
Sbjct: 228 ERVANDEAKIDEYIDGLIDPNADAEAAAQAAADEDEEFEDEEAEEVGDEEEDEDDEGAGG 287

Query: 232 ---STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
              S  QLE+LK  +L++FS I   FDKMR+AFEKEGY S+ Y+KA  +I NE++ IRFT
Sbjct: 288 AAASARQLEELKQAALVRFSVIGDQFDKMRRAFEKEGYKSKPYLKAQESIQNELMAIRFT 347

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+D+    
Sbjct: 348 ARTVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRGDFVSRFPGNETNLRWIDSVVAD 407

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEA
Sbjct: 408 GKPYSAIVERNIPAVHELQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEA 467

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 468 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 527

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 528 IADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAK 587

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 588 EPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMR 647

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 648 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 684


>gi|445495926|ref|ZP_21462970.1| RNA polymerase sigma factor RpoD [Janthinobacterium sp. HH01]
 gi|444792087|gb|ELX13634.1| RNA polymerase sigma factor RpoD [Janthinobacterium sp. HH01]
          Length = 830

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/630 (64%), Positives = 493/630 (78%), Gaps = 19/630 (3%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
               D KS + EE+E  R + K LI +GKERG+LT++EIND LPE+I+D E IE II TF 
Sbjct: 201  LGVDSKSTA-EELERRRTQIKNLINMGKERGFLTYAEINDQLPENIVDPEAIEGIIATFN 259

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M I++ E   D E+L+L++    +TSDD+VE A   ALSTVDSDFGRT DP++MYMREM
Sbjct: 260  DMGIAIYERAPDAESLLLTDSVATVTSDDEVEAAAATALSTVDSDFGRTTDPVRMYMREM 319

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+V LLTR+GEIEIAKRIE GLKDMI AIS+CPTTI EI+  A KI  +E+K+DE+VDG 
Sbjct: 320  GAVALLTREGEIEIAKRIEGGLKDMIQAISACPTTIAEIVALAKKIEADELKVDEVVDGF 379

Query: 990  IDKNFSSNNRVIKGNKNNNEEKIL------------IESSSADLSTEQLEKLKYESLIKF 1037
            +D N ++N   +        ++                  +A  STEQL +LK  +L KF
Sbjct: 380  VDLNEANNAPAVSAAPAVASDEDEEEEEEVEEEDGDANGGAAGFSTEQLAQLKKAALEKF 439

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              IS  +DKMRKA    GY S++Y+ A   IS E+LGIRFTAK +EKLCDTLR Q+ +V 
Sbjct: 440  DVISTQYDKMRKA--AGGYGSKAYVAAQEAISAELLGIRFTAKVVEKLCDTLRGQMEEVR 497

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
             IE+ +LE+ VNKCGMPR HFIKVFP NE +L+WVD E    + Y+ IL RN+P++KELQ
Sbjct: 498  HIERAVLELCVNKCGMPRAHFIKVFPGNECDLDWVDGEVDSAYPYSAILGRNVPAVKELQ 557

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            +K+I+LQ  + LPL DLR IN++M AGE +AR+AKREMT ANLRLVISIAKKY +RGLQF
Sbjct: 558  KKMIDLQARVALPLADLRKINKQMAAGEKRARQAKREMTVANLRLVISIAKKYINRGLQF 617

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWIRQAITRSIAD ARTIR+PVHMIETIN
Sbjct: 618  LDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWIRQAITRSIADMARTIRVPVHMIETIN 677

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQI+QETGSEPD + +A+KMEMPE K+R+IMKIAKEP+SME+P+G+D DS LGD
Sbjct: 678  KMNRISRQIMQETGSEPDLATLAVKMEMPENKVREIMKIAKEPISMETPMGEDGDSQLGD 737

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED   LAP DAAL+ASMR+V+K++L+SLTPRE+KVLRMR+G+EMS+DHTLEEVGKQFD
Sbjct: 738  FIEDNTTLAPLDAALHASMRNVIKEVLDSLTPREAKVLRMRYGVEMSNDHTLEEVGKQFD 797

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            VTRERIRQIEAKA+ KLR PSR  KLK FL
Sbjct: 798  VTRERIRQIEAKAMSKLRQPSRSDKLKTFL 827



 Score =  822 bits (2122), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/633 (63%), Positives = 491/633 (77%), Gaps = 20/633 (3%)

Query: 24  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 83
              D KS + EE+E  R + K LI +GKERG+LT++EIND LPE+I+D E IE II TF 
Sbjct: 201 LGVDSKSTA-EELERRRTQIKNLINMGKERGFLTYAEINDQLPENIVDPEAIEGIIATFN 259

Query: 84  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 139
            M I++ E   D E+L+L++    +TSDD+VE A   ALSTVDSDFGRT DP++MYMREM
Sbjct: 260 DMGIAIYERAPDAESLLLTDSVATVTSDDEVEAAAATALSTVDSDFGRTTDPVRMYMREM 319

Query: 140 GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 199
           G+V LLTR+GEIEIAKRIE GLKDMI AIS+CPTTI EI+  A KI  +E+K+DE+VDG 
Sbjct: 320 GAVALLTREGEIEIAKRIEGGLKDMIQAISACPTTIAEIVALAKKIEADELKVDEVVDGF 379

Query: 200 IDKNFSSNNRVIKGNKNNNEEKIL------------IESSSADLSTEQLEKLKYESLIKF 247
           +D N ++N   +        ++                  +A  STEQL +LK  +L KF
Sbjct: 380 VDLNEANNAPAVSAAPAVASDEDEEEEEEVEEEDGDANGGAAGFSTEQLAQLKKAALEKF 439

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
             IS  +DKMRKA    GY S++Y+ A   IS E+LGIRFTAK +EKLCDTLR Q+ +V 
Sbjct: 440 DVISTQYDKMRKA--AGGYGSKAYVAAQEAISAELLGIRFTAKVVEKLCDTLRGQMEEVR 497

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
            IE+ +LE+ VNKCGMPR HFIKVFP NE +L+WVD E    + Y+ IL RN+P++KELQ
Sbjct: 498 HIERAVLELCVNKCGMPRAHFIKVFPGNECDLDWVDGEVDSAYPYSAILGRNVPAVKELQ 557

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           +K+I+LQ  + LPL DLR IN++M AGE +AR+AKREMT ANLRLVISIAKKY +RGLQF
Sbjct: 558 KKMIDLQARVALPLADLRKINKQMAAGEKRARQAKREMTVANLRLVISIAKKYINRGLQF 617

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWIRQAITRSIAD ARTIR+PVHMIETIN
Sbjct: 618 LDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWIRQAITRSIADMARTIRVPVHMIETIN 677

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQI+QETGSEPD + +A+KMEMPE K+R+IMKIAKEP+SME+P+G+D DS LGD
Sbjct: 678 KMNRISRQIMQETGSEPDLATLAVKMEMPENKVREIMKIAKEPISMETPMGEDGDSQLGD 737

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED   LAP DAAL+ASMR+V+K++L+SLTPRE+KVLRMR+G+EMS+DHTLEEVGKQFD
Sbjct: 738 FIEDNTTLAPLDAALHASMRNVIKEVLDSLTPREAKVLRMRYGVEMSNDHTLEEVGKQFD 797

Query: 608 VTRERIRQIEAKALRKLR-PLAHDWLEQRTHQN 639
           VTRERIRQIEAKA+ KLR P   D L+    QN
Sbjct: 798 VTRERIRQIEAKAMSKLRQPSRSDKLKTFLTQN 830


>gi|113868683|ref|YP_727172.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha H16]
 gi|113527459|emb|CAJ93804.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia eutropha
            H16]
          Length = 827

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/629 (65%), Positives = 499/629 (79%), Gaps = 18/629 (2%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T   + I+
Sbjct: 198  QQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 257

Query: 879  VSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 258  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 317

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  A++++ +EIKIDE VDGLID N 
Sbjct: 318  LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVDGLIDPNA 377

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLST--------------EQLEKLKYESLIKFSNI 1040
                          +++ +      +                  QLE+LK  +L KF  I
Sbjct: 378  DEAPEAPAAPAAAADDEDIESDDEEEGDEDDDDEGGAGAGASARQLEELKQNALEKFRVI 437

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            +  FDKMR+AFEKEGYNS+ Y+KA   I  E++GIRFTA+++E+LCDTLR Q+++V ++E
Sbjct: 438  AEQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIRFTARNVERLCDTLRGQVDEVRKLE 497

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + IL IVV+KCGMPR  F+  FP NE NL WV         Y+ I+ RN+P++ ELQQKL
Sbjct: 498  RSILNIVVDKCGMPRSEFVARFPGNETNLEWVHTIVADGKGYSTIVERNVPAVHELQQKL 557

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            I+LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDL
Sbjct: 558  IDLQSRVVLPLKELKGVNRKMAEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDL 617

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 618  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 677

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 678  RISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIE 737

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTR
Sbjct: 738  DTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTR 797

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            ERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 798  ERIRQIEAKALRKLRHPSRSDKLKSFLEG 826



 Score =  821 bits (2120), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/639 (63%), Positives = 500/639 (78%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   +  + EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 175 TEKQKAKDRKAKEKALLKEFA-STQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDH 233

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 234 LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 293

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 294 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 353

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLST------- 233
            A++++ +EIKIDE VDGLID N               +++ +      +          
Sbjct: 354 HAERVANDEIKIDEFVDGLIDPNADEAPEAPAAPAAAADDEDIESDDEEEGDEDDDDEGG 413

Query: 234 -------EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                   QLE+LK  +L KF  I+  FDKMR+AFEKEGYNS+ Y+KA   I  E++GIR
Sbjct: 414 AGAGASARQLEELKQNALEKFRVIAEQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIR 473

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL WV    
Sbjct: 474 FTARNVERLCDTLRGQVDEVRKLERSILNIVVDKCGMPRSEFVARFPGNETNLEWVHTIV 533

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
                Y+ I+ RN+P++ ELQQKLI+LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMT
Sbjct: 534 ADGKGYSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKGVNRKMAEGERRAREAKREMT 593

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 594 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 653

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 654 RSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKI 713

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLR
Sbjct: 714 AKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLR 773

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 774 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 812


>gi|309781724|ref|ZP_07676457.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
 gi|308919365|gb|EFP65029.1| RNA polymerase sigma factor RpoD [Ralstonia sp. 5_7_47FAA]
          Length = 821

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/632 (64%), Positives = 502/632 (79%), Gaps = 16/632 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +E+++ T  
Sbjct: 189  FAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDVESLETLVATLN 248

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 249  DIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 308

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 309  GTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 368

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL------------STEQLEKLKYESLIKF 1037
            ID N  ++       +   EE+   E    +             S  QLE+LK  +L+KF
Sbjct: 369  IDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGAAAASARQLEELKQAALLKF 428

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++V 
Sbjct: 429  GVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFTARNVERLCDTLRGQVDEVR 488

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            ++E+ IL IVV+KCGMPR  F+  FP NE NL W++        Y+ I+ RN+P++ ELQ
Sbjct: 489  KLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVADGKPYSTIVERNVPAVHELQ 548

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQF
Sbjct: 549  QKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQF 608

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 609  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 668

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 669  KMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 728

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFD
Sbjct: 729  FIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFD 788

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 789  VTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 820



 Score =  820 bits (2119), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/637 (63%), Positives = 501/637 (78%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 170 TEKLKARDRKAKEKALLKEFAASQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDH 229

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E +E+++ T   + ++V E   D ETL+L++    +T++++ EE  EAALST
Sbjct: 230 LPDDMVDVESLETLVATLNDIGVAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALST 289

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 290 VDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILA 349

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL--------- 231
             ++++ +E KIDE +DGLID N  ++       +   EE+   E    +          
Sbjct: 350 MGERVANDEAKIDEYIDGLIDPNAEADAAAAAEEEEEFEEEEAEEEGDEEEDEDDEGAGA 409

Query: 232 ---STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
              S  QLE+LK  +L+KF  I   FDKMR+AFEKEGY S+ Y+KA   I  E++ IRFT
Sbjct: 410 AAASARQLEELKQAALLKFGVIGEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTIRFT 469

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           A+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W++     
Sbjct: 470 ARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRSDFVARFPGNETNLKWIETVVAD 529

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ I+ RN+P++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEA
Sbjct: 530 GKPYSTIVERNVPAVHELQQKLIDLQARVVLPLTELKDVNRKMSEGERRAREAKREMTEA 589

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 590 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 649

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAK
Sbjct: 650 IADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAK 709

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 710 EPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMR 769

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 770 FGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806


>gi|126443442|ref|YP_001063518.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126222933|gb|ABN86438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 736

 Score =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/636 (65%), Positives = 505/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 101  KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 159

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 160  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 219

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 220  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 279

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 280  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 339

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 340  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 399

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 400  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYGAILSRNIPAI 459

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 460  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 519

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 520  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 579

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 580  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 639

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 640  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 699

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 700  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 735



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/639 (64%), Positives = 505/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 84  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 142

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 143 HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 202

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 203 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 262

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 263 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 322

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 323 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 382

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 383 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIA 442

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 443 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 502

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 503 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 562

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 563 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 622

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 623 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 682

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 683 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 721


>gi|167566502|ref|ZP_02359418.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis EO147]
 gi|167573583|ref|ZP_02366457.1| RNA polymerase sigma factor RpoD [Burkholderia oklahomensis C6786]
          Length = 681

 Score =  835 bits (2156), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/636 (65%), Positives = 507/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 46   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 104

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 105  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 164

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 165  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 224

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N +  +                       E +    ++ A  +  QLE LK  S
Sbjct: 225  DGLIDPNAADADGFSEKDAEEIENEDEEAEENEEEEAEDDDGAAQASANAAQLEALKRAS 284

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 285  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 344

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +      H Y+ IL RNIP+I
Sbjct: 345  DEVRQVERQILHIVVDKCGMPRSEFIARFPSNETDLDWAEKIAAEGHSYSAILSRNIPAI 404

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 405  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 464

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 465  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 524

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 525  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 584

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 585  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 644

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 645  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/639 (64%), Positives = 507/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 29  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 87

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 88  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 147

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 148 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 207

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIES 226
             A++++  E ++DE+VDGLID N +  +                       E +    +
Sbjct: 208 AMAERVANEESRVDELVDGLIDPNAADADGFSEKDAEEIENEDEEAEENEEEEAEDDDGA 267

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 268 AQASANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 327

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +   
Sbjct: 328 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPSNETDLDWAEKIA 387

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 388 AEGHSYSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 447

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 448 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 507

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 508 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 567

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 568 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 627

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|186472768|ref|YP_001860110.1| RNA polymerase sigma factor RpoD [Burkholderia phymatum STM815]
 gi|184195100|gb|ACC73064.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum STM815]
          Length = 685

 Score =  835 bits (2156), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 426/636 (66%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 50   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 108

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 109  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 168

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 169  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 228

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------LEKLKYES 1033
            DGLID N      FS        +++  EE+   E    D    Q       LE+LK  S
Sbjct: 229  DGLIDVNAEDTDGFSEQEAEAIESEDEEEEEADEEEEEDDDGAAQATANAAQLEELKRLS 288

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+
Sbjct: 289  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIRFTARTVERLCDTLRAQV 348

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP NE +L W D      H Y+ IL RN+P+I
Sbjct: 349  DEVRQVERQILHTVVDKCGMPRAEFIARFPGNETDLEWADKIVSENHAYSAILSRNVPAI 408

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 409  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 468

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 469  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 528

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 529  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 588

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 589  HLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 648

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 649  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 684



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/639 (65%), Positives = 509/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND
Sbjct: 33  GEKAKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEIND 91

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALS 119
            LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALS
Sbjct: 92  HLPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALS 151

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL
Sbjct: 152 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADIL 211

Query: 180 IAADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLST 233
             A++++  EI+IDE+VDGLID N      FS        +++  EE+   E    D   
Sbjct: 212 AMAERVANEEIRIDELVDGLIDVNAEDTDGFSEQEAEAIESEDEEEEEADEEEEEDDDGA 271

Query: 234 EQ-------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
            Q       LE+LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IR
Sbjct: 272 AQATANAAQLEELKRLSLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIR 331

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP NE +L W D   
Sbjct: 332 FTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGNETDLEWADKIV 391

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 392 SENHAYSAILSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 451

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 452 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 511

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 512 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 571

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 572 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLR 631

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 632 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 670


>gi|422321719|ref|ZP_16402764.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
 gi|317403353|gb|EFV83866.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
          Length = 813

 Score =  835 bits (2156), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/615 (66%), Positives = 496/615 (80%), Gaps = 9/615 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 202  SAEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 261

Query: 882  HVLDTETLMLSN---ITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELL 935
               D ETL++S    + S+DD ++  + A   L+TVDSDFGRT DP++MYMREMGSVELL
Sbjct: 262  QAPDAETLLMSENAPVASNDDDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELL 321

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D    
Sbjct: 322  TREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQAQIDEVVDGLVD---P 378

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
             +     G   + +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+G
Sbjct: 379  EDGEEYAGAGVSADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDG 438

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y S+ Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR
Sbjct: 439  YKSDIYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPR 498

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             HFIKVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+
Sbjct: 499  THFIKVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLK 558

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            D+N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 559  DVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 618

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPD
Sbjct: 619  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 678

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ S
Sbjct: 679  PATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGS 738

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            MR VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 739  MRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 798

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  KLK FLEG+
Sbjct: 799  HPSRADKLKSFLEGQ 813



 Score =  812 bits (2098), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/600 (65%), Positives = 484/600 (80%), Gaps = 9/600 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K LIKLGK+RGYLT+ EIND LP+D++D E I+ II TF  M I+V +
Sbjct: 202 SAEEYEARRNRLKQLIKLGKDRGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGIAVYD 261

Query: 92  HVLDTETLMLSN---ITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELL 145
              D ETL++S    + S+DD ++  + A   L+TVDSDFGRT DP++MYMREMGSVELL
Sbjct: 262 QAPDAETLLMSENAPVASNDDDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGSVELL 321

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+GEIEIAKRIE+GLK M+ AIS+CPTTI EIL    ++ + + +IDE+VDGL+D    
Sbjct: 322 TREGEIEIAKRIEDGLKHMVMAISACPTTINEILAHVLRVREGQAQIDEVVDGLVD---P 378

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
            +     G   + +E    +  +  +S++QLE L+ ++L KF  +   FDKMR ++EK+G
Sbjct: 379 EDGEEYAGAGVSADEDESDDGPAGGMSSKQLEDLRVKALAKFDEVGKQFDKMRLSYEKDG 438

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           Y S+ Y++A  +I NE++GIRFTAK +EKL DTLRNQ+ +V Q+E+ +L   V++ GMPR
Sbjct: 439 YKSDIYVRAQESIQNELMGIRFTAKMVEKLADTLRNQVEEVRQLERAVLHTCVDRAGMPR 498

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            HFIKVFP NE NL WV +E    H Y   L R IP+++ELQQKLI+LQT +VLPL DL+
Sbjct: 499 THFIKVFPGNETNLQWVVDEVAAGHPYAETLERQIPAVQELQQKLIDLQTRVVLPLKDLK 558

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           D+N++M  GE KARKAKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 559 DVNKRMATGEAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 618

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPD
Sbjct: 619 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPD 678

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAPSDAAL+ S
Sbjct: 679 PATLAQKMDMPEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTSTLAPSDAALHGS 738

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MR VVK++L+SLTPRE+KVLRMRFGIEMS+D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 739 MRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 798


>gi|254248772|ref|ZP_04942092.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
 gi|124875273|gb|EAY65263.1| Sigma-70 region 1.1 [Burkholderia cenocepacia PC184]
          Length = 805

 Score =  835 bits (2156), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/640 (65%), Positives = 511/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS--------TEQLEKL 1029
            DGL+D N         FS+       N++   E+   E    +            QLE L
Sbjct: 345  DGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 404

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTL
Sbjct: 405  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTL 464

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 465  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKITAEGHPYSAVLSRN 524

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEA+LRLVISIAKK
Sbjct: 525  VPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEAHLRLVISIAKK 584

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 585  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 644

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 645  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 704

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 705  DDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 764

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  822 bits (2124), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/641 (64%), Positives = 512/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS 232
           A++++  EI++DE+VDGL+D N         FS+       N++   E+   E    +  
Sbjct: 330 AERVANEEIRVDELVDGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 389

Query: 233 --------TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
                     QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ 
Sbjct: 390 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMT 449

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 450 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 509

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 510 ITAEGHPYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 569

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEA+LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 570 MTEAHLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 629

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 630 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 689

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 690 KIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKV 749

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|421866277|ref|ZP_16297949.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia H111]
 gi|444369210|ref|ZP_21168979.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia
            K56-2Valvano]
 gi|358073860|emb|CCE48827.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia H111]
 gi|443599506|gb|ELT67779.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia
            K56-2Valvano]
          Length = 683

 Score =  834 bits (2154), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/640 (65%), Positives = 511/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 222

Query: 987  DGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS--------TEQLEKL 1029
            DGL+D N         FS+       N++   E+   E    +            QLE L
Sbjct: 223  DGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 282

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTL
Sbjct: 283  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTL 342

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +  T   H Y+ +L RN
Sbjct: 343  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKITAEGHSYSAVLSRN 402

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 403  VPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 462

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 463  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 522

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 523  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 582

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 583  DDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 642

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682



 Score =  822 bits (2124), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/641 (64%), Positives = 512/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS 232
           A++++  EI++DE+VDGL+D N         FS+       N++   E+   E    +  
Sbjct: 208 AERVANEEIRVDELVDGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 267

Query: 233 --------TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
                     QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ 
Sbjct: 268 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMT 327

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W + 
Sbjct: 328 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEK 387

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 388 ITAEGHSYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 447

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 448 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 507

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 508 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 567

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 568 KIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKV 627

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|402569601|ref|YP_006618945.1| RNA polymerase sigma factor RpoD [Burkholderia cepacia GG4]
 gi|402250798|gb|AFQ51251.1| RNA polymerase sigma factor RpoD [Burkholderia cepacia GG4]
          Length = 683

 Score =  834 bits (2154), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/640 (65%), Positives = 512/640 (80%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 222

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 223  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 282

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 283  KRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTL 342

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 343  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVTAEGHAYSAVLTRN 402

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+LI+LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 403  VPAIREQQQRLIDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 462

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 463  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 522

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 523  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 582

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 583  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 642

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682



 Score =  822 bits (2123), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/641 (64%), Positives = 513/641 (80%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 208 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 267

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ 
Sbjct: 268 GAAQASANAAQLEALKRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMT 327

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 328 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 387

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+LI+LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 388 VTAEGHAYSAVLTRNVPAIREQQQRLIDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 447

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 448 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 507

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 508 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 567

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 568 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 627

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|167842198|ref|ZP_02468882.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis MSMB43]
 gi|424905498|ref|ZP_18329001.1| hypothetical protein A33K_16885 [Burkholderia thailandensis MSMB43]
 gi|390928391|gb|EIP85795.1| hypothetical protein A33K_16885 [Burkholderia thailandensis MSMB43]
          Length = 680

 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/636 (65%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 45   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 223

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N + ++                    +  EE     ++ A  +  QLE LK  S
Sbjct: 224  DGLIDPNAADSDGFSEKDAEEIENEDEEAEEGDEEEEDEDDGAAQATANAAQLEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ IL RNIP+I
Sbjct: 344  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYSAILSRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  820 bits (2119), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/639 (64%), Positives = 509/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIES 226
             A++++  E ++DE+VDGLID N + ++                    +  EE     +
Sbjct: 207 AMAERVANEESRVDELVDGLIDPNAADSDGFSEKDAEEIENEDEEAEEGDEEEEDEDDGA 266

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHSYSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|299066184|emb|CBJ37368.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CMR15]
          Length = 777

 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/632 (64%), Positives = 504/632 (79%), Gaps = 16/632 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 145  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 204

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 205  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 264

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 265  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 324

Query: 990  IDKNFSSNN------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKF 1037
            ID N  +                     +  E++    +  A  S  QLE+LK  +L KF
Sbjct: 325  IDPNADAAEAQAGDEDEDFEDEDADEGDDEEEDEDDDGAGGAAASARQLEELKQAALAKF 384

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + I+  F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V 
Sbjct: 385  AIIADQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVR 444

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            ++E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQ
Sbjct: 445  KLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQ 504

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQF
Sbjct: 505  QKLIDLQARVVLPLAELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQF 564

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 565  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 624

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 625  KMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 684

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFD
Sbjct: 685  FIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFD 744

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 745  VTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 776



 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/635 (63%), Positives = 502/635 (79%), Gaps = 16/635 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 128 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 187

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 188 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 247

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 248 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 307

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNN------------RVIKGNKNNNEEKILIESSSAD 230
           ++++ +E KIDE +DGLID N  +                     +  E++    +  A 
Sbjct: 308 ERVANDEAKIDEYIDGLIDPNADAAEAQAGDEDEDFEDEDADEGDDEEEDEDDDGAGGAA 367

Query: 231 LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
            S  QLE+LK  +L KF+ I+  F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA+
Sbjct: 368 ASARQLEELKQAALAKFAIIADQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTAR 427

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
           ++E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++       
Sbjct: 428 NVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGK 487

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANL
Sbjct: 488 PYSAIVERNIPAVHELQQKLIDLQARVVLPLAELKDVNRKMSEGERRAREAKREMTEANL 547

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 548 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 607

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP
Sbjct: 608 DQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEP 667

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFG
Sbjct: 668 ISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFG 727

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 728 IEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 762


>gi|221197050|ref|ZP_03570097.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
 gi|221203722|ref|ZP_03576740.1| sigma-70, non-essential region family [Burkholderia multivorans CGD2]
 gi|421468342|ref|ZP_15916894.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
            BAA-247]
 gi|221175888|gb|EEE08317.1| sigma-70, non-essential region family [Burkholderia multivorans CGD2]
 gi|221183604|gb|EEE16004.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD2M]
 gi|400232197|gb|EJO61833.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans ATCC
            BAA-247]
          Length = 682

 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/639 (65%), Positives = 513/639 (80%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++ +EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELV 222

Query: 987  DGLIDKNFSSNN----------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N S  +                  ++  +   EE+    ++ A  +  QLE LK
Sbjct: 223  DGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEALK 282

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
              SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ IRFTA+++E+LCDTLR
Sbjct: 283  RASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTIRFTARTVERLCDTLR 342

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +      H Y+ IL RNI
Sbjct: 343  AQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKIAAEGHSYSAILSRNI 402

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKY
Sbjct: 403  PAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKY 462

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 463  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 522

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 523  HMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDD 582

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 583  DDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 642

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score =  820 bits (2118), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/640 (64%), Positives = 513/640 (80%), Gaps = 22/640 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKARDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNN----------------RVIKGNKNNNEEKILIE 225
           A++++ +EI++DE+VDGL+D N S  +                  ++  +   EE+    
Sbjct: 208 AERVANDEIRVDELVDGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDG 267

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++ A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ I
Sbjct: 268 AAQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTI 327

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +  
Sbjct: 328 RFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKI 387

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
               H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREM
Sbjct: 388 AAEGHSYSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREM 447

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 448 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 507

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 508 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMK 567

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVL
Sbjct: 568 IAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>gi|107026824|ref|YP_624335.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia AU 1054]
 gi|105896198|gb|ABF79362.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia AU
            1054]
          Length = 805

 Score =  833 bits (2153), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/640 (65%), Positives = 512/640 (80%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 345  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 404

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTL
Sbjct: 405  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTL 464

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 465  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKITAEGHPYSAVLSRN 524

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 525  VPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 584

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 585  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 644

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 645  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 704

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAA +ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 705  DDDSHLGDFIEDTNTVAPADAAPHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 764

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 765  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/641 (64%), Positives = 513/641 (80%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 330 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 389

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ 
Sbjct: 390 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMT 449

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 450 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 509

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 510 ITAEGHPYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 569

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 570 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 629

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 630 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 689

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA +ASMR VVKD+L+SLTPRE+KV
Sbjct: 690 KIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAAPHASMRDVVKDVLDSLTPREAKV 749

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 750 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|53716429|ref|YP_105146.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|53722776|ref|YP_111761.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|67643221|ref|ZP_00441969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|124381664|ref|YP_001025512.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
 gi|126447609|ref|YP_001077577.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134278673|ref|ZP_01765387.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167000270|ref|ZP_02266089.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|167743532|ref|ZP_02416306.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|167820721|ref|ZP_02452401.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
 gi|167850557|ref|ZP_02476065.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|167899150|ref|ZP_02486551.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 7894]
 gi|167907493|ref|ZP_02494698.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei NCTC
            13177]
 gi|167915832|ref|ZP_02502923.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 112]
 gi|167923671|ref|ZP_02510762.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei BCC215]
 gi|217422551|ref|ZP_03454054.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|226195650|ref|ZP_03791237.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pakistan
            9]
 gi|237508723|ref|ZP_04521438.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei MSHR346]
 gi|242312268|ref|ZP_04811285.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254177429|ref|ZP_04884085.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254186160|ref|ZP_04892678.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
            52237]
 gi|254194055|ref|ZP_04900487.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|254203084|ref|ZP_04909446.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208417|ref|ZP_04914766.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254265453|ref|ZP_04956318.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|254301213|ref|ZP_04968657.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|254359397|ref|ZP_04975669.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|386865564|ref|YP_006278512.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1026b]
 gi|403523631|ref|YP_006659200.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei BPC006]
 gi|418397007|ref|ZP_12970757.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 354a]
 gi|418536785|ref|ZP_13102454.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1026a]
 gi|418544096|ref|ZP_13109408.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1258a]
 gi|418550937|ref|ZP_13115884.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1258b]
 gi|418556604|ref|ZP_13121228.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 354e]
 gi|52213190|emb|CAH39230.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei K96243]
 gi|52422399|gb|AAU45969.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|126240463|gb|ABO03575.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|134250457|gb|EBA50537.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|147746129|gb|EDK53207.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147751104|gb|EDK58172.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148028584|gb|EDK86544.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|157811356|gb|EDO88526.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157933846|gb|EDO89516.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
            52237]
 gi|160698469|gb|EDP88439.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|169650806|gb|EDS83499.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|217394782|gb|EEC34801.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|225932135|gb|EEH28135.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pakistan
            9]
 gi|235000928|gb|EEP50352.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei MSHR346]
 gi|238524506|gb|EEP87939.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|242135507|gb|EES21910.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|243063759|gb|EES45945.1| RNA polymerase sigma factor RpoD [Burkholderia mallei PRL-20]
 gi|254216455|gb|EET05840.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|261826434|gb|ABM99450.2| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10229]
 gi|385350368|gb|EIF56912.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1258b]
 gi|385350765|gb|EIF57287.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1258a]
 gi|385351677|gb|EIF58143.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1026a]
 gi|385366769|gb|EIF72371.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 354e]
 gi|385369571|gb|EIF74886.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 354a]
 gi|385662692|gb|AFI70114.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1026b]
 gi|403078698|gb|AFR20277.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei BPC006]
          Length = 680

 Score =  833 bits (2152), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/636 (65%), Positives = 505/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 45   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 224  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 344  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/639 (64%), Positives = 505/639 (79%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 207 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 266

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|221212356|ref|ZP_03585333.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|421476918|ref|ZP_15924771.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CF2]
 gi|221167455|gb|EED99924.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|400227233|gb|EJO57240.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CF2]
          Length = 682

 Score =  833 bits (2152), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/639 (65%), Positives = 513/639 (80%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++ +EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRVDELV 222

Query: 987  DGLIDKNFSSNN----------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N S  +                  ++  +   EE+    ++ A  +  QLE LK
Sbjct: 223  DGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDGAAQATANAAQLEALK 282

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
              SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ IRFTA+++E+LCDTLR
Sbjct: 283  RASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTIRFTARTVERLCDTLR 342

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +      H Y+ IL RNI
Sbjct: 343  AQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKIAAEGHSYSAILSRNI 402

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKY
Sbjct: 403  PAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKY 462

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 463  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 522

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 523  HMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDD 582

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 583  DDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 642

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/640 (64%), Positives = 514/640 (80%), Gaps = 22/640 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNN----------------RVIKGNKNNNEEKILIE 225
           A++++ +EI++DE+VDGL+D N S  +                  ++  +   EE+    
Sbjct: 208 AERVANDEIRVDELVDGLLDPNASDTDTDGFSAKEAEEIENEDEEVEEEEEEEEEEDDDG 267

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++ A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ I
Sbjct: 268 AAQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTI 327

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +  
Sbjct: 328 RFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKI 387

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
               H Y+ IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREM
Sbjct: 388 AAEGHSYSAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREM 447

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 448 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 507

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 508 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMK 567

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVL
Sbjct: 568 IAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>gi|134292973|ref|YP_001116709.1| RNA polymerase sigma factor RpoD [Burkholderia vietnamiensis G4]
 gi|134136130|gb|ABO57244.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia vietnamiensis
            G4]
          Length = 809

 Score =  833 bits (2151), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/640 (65%), Positives = 507/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E +E II 
Sbjct: 170  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYGEINDHLPDNFTETEALEGIIG 228

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 229  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 288

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 289  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 348

Query: 987  DGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQ--------LEKL 1029
            DGL+D N         FS+       N++   E+   E    D             LE L
Sbjct: 349  DGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEAL 408

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 409  KRASLEKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTL 468

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RN
Sbjct: 469  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRN 528

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 529  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 588

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 589  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 648

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 649  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 708

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 709  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 768

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 769  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 808



 Score =  821 bits (2120), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/641 (64%), Positives = 508/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT+ EIND L
Sbjct: 155 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYGEINDHL 213

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 214 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 273

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 274 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 333

Query: 182 ADKISKNEIKIDEIVDGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS 232
           A++++  EI++DE+VDGL+D N         FS+       N++   E+   E    D  
Sbjct: 334 AERVANEEIRVDELVDGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDD 393

Query: 233 TEQ--------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
                      LE LK  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ 
Sbjct: 394 GAAQATANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMT 453

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 454 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 513

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
                H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 514 IAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 573

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 574 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 633

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 634 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 693

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 694 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 753

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 754 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 794


>gi|413965117|ref|ZP_11404343.1| RNA polymerase sigma factor RpoD [Burkholderia sp. SJ98]
 gi|413927791|gb|EKS67080.1| RNA polymerase sigma factor RpoD [Burkholderia sp. SJ98]
          Length = 681

 Score =  832 bits (2150), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 420/637 (65%), Positives = 506/637 (79%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 45   KDAFSSS-APGTVEELEERRGKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 103

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A+++   E+++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVQNEEVRVDELV 223

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYE 1032
            DGLID N      FS        ++     +   E    +         +  QLE LK +
Sbjct: 224  DGLIDPNAQDTDGFSEQEAEAIESEEEETAEEGEEEEEEEDDGSAQASANAAQLEALKLQ 283

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KF+ IS  FDKMR+A+EKEGY S++Y+KA   I  E++ IRFTA+++E+LCDTLR Q
Sbjct: 284  SLEKFALISEWFDKMRRAYEKEGYKSKAYLKAQEAIQTELMNIRFTARTVERLCDTLRAQ 343

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V Q+E+QIL  VV+KCGMPR  FI  FP NE +L W D      H+Y+ +L RNIP+
Sbjct: 344  VDEVRQVERQILHTVVDKCGMPRAEFITRFPGNETDLEWSDKVVAEGHEYSAVLERNIPA 403

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 404  IREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 463

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 464  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 523

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 524  IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 583

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 584  SHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 643

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score =  818 bits (2114), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/639 (64%), Positives = 506/639 (79%), Gaps = 20/639 (3%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND 
Sbjct: 29  EKAKARDRRAKEKALLKDAFSSS-APGTVEELEERRGKLRALIKLGKERGFLTYGEINDH 87

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALST
Sbjct: 88  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALST 147

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 148 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 207

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSAD---- 230
            A+++   E+++DE+VDGLID N      FS        ++     +   E    +    
Sbjct: 208 MAERVQNEEVRVDELVDGLIDPNAQDTDGFSEQEAEAIESEEEETAEEGEEEEEEEDDGS 267

Query: 231 ----LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                +  QLE LK +SL KF+ IS  FDKMR+A+EKEGY S++Y+KA   I  E++ IR
Sbjct: 268 AQASANAAQLEALKLQSLEKFALISEWFDKMRRAYEKEGYKSKAYLKAQEAIQTELMNIR 327

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP NE +L W D   
Sbjct: 328 FTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFITRFPGNETDLEWSDKVV 387

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H+Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 388 AEGHEYSAVLERNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 447

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 448 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 507

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 508 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 567

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 568 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLR 627

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|170699447|ref|ZP_02890491.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
            IOP40-10]
 gi|170135647|gb|EDT03931.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
            IOP40-10]
          Length = 683

 Score =  832 bits (2149), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/640 (65%), Positives = 511/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 222

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 223  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEAL 282

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 283  KRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTL 342

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RN
Sbjct: 343  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRN 402

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 403  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 462

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 463  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 522

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 523  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 582

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 583  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 642

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682



 Score =  820 bits (2118), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/641 (64%), Positives = 512/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 208 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDD 267

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ 
Sbjct: 268 GAAQATANAAQLEALKRASLDKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMT 327

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 328 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 387

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
                H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 388 IAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 447

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 448 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 507

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 508 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 567

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 568 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 627

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|170736023|ref|YP_001777283.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia MC0-3]
 gi|169818211|gb|ACA92793.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
            MC0-3]
          Length = 683

 Score =  832 bits (2148), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/640 (65%), Positives = 513/640 (80%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 222

Query: 987  DGLIDKNFSSN-----------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKL 1029
            DGL+D N S +                 +   +  +   EE+    ++ A  +  QLE L
Sbjct: 223  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEAL 282

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTL
Sbjct: 283  KRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTL 342

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  T   H Y+ +L RN
Sbjct: 343  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKITAEGHPYSAVLSRN 402

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 403  VPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 462

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 463  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 522

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 523  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 582

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 583  DDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 642

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 682



 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/641 (64%), Positives = 514/641 (80%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-----------------NRVIKGNKNNNEEKILI 224
           A++++  EI++DE+VDGL+D N S +                 +   +  +   EE+   
Sbjct: 208 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEDD 267

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
            ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I +E++ 
Sbjct: 268 GAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMT 327

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 328 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 387

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 388 ITAEGHPYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 447

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 448 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 507

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 508 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 567

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 568 KIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKV 627

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|416995857|ref|ZP_11939116.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
 gi|325518128|gb|EGC97914.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
          Length = 682

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/639 (65%), Positives = 511/639 (79%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 44   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 102

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 103  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 162

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 163  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 222

Query: 987  DGLIDKNFSSNN----------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N S  +                   +  +   EE+    ++ A  +  QLE LK
Sbjct: 223  DGLLDPNASDTDTDGFSAKEAEEIENEDEDAEEEEEEEEEEDDDGAAQATANAAQLEALK 282

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
              SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ IRFTA+++E+LCDTLR
Sbjct: 283  RASLEKFAQISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTIRFTARTVERLCDTLR 342

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RNI
Sbjct: 343  AQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRNI 402

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKY
Sbjct: 403  PAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKY 462

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 463  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 522

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 523  HMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDD 582

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 583  DDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 642

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 643  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/640 (64%), Positives = 512/640 (80%), Gaps = 22/640 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 29  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 87

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 88  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 147

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 148 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 207

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNN----------------RVIKGNKNNNEEKILIE 225
           A++++  EI++DE+VDGL+D N S  +                   +  +   EE+    
Sbjct: 208 AERVANEEIRVDELVDGLLDPNASDTDTDGFSAKEAEEIENEDEDAEEEEEEEEEEDDDG 267

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++ A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I +E++ I
Sbjct: 268 AAQATANAAQLEALKRASLEKFAQISEWFDKMRRAFEKEGYKSKSYLKAQETIQSELMTI 327

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  
Sbjct: 328 RFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKI 387

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
               H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREM
Sbjct: 388 AAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREM 447

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 448 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 507

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 508 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMK 567

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVL
Sbjct: 568 IAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>gi|390577041|ref|ZP_10257081.1| RNA polymerase sigma factor RpoD [Burkholderia terrae BS001]
 gi|389931019|gb|EIM93107.1| RNA polymerase sigma factor RpoD [Burkholderia terrae BS001]
          Length = 682

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/636 (66%), Positives = 509/636 (80%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 47   KDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 105

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 106  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 165

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A++++  EI+IDE+V
Sbjct: 166  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVANEEIRIDELV 225

Query: 987  DGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYES 1033
            DGLID N    +                +   +  EE+    ++ A  +  QLE+LK  S
Sbjct: 226  DGLIDTNAEDTDGFSEQEAEAIENEEEEEAEADEEEEEDDDGAAQATANAAQLEELKRMS 285

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+
Sbjct: 286  LEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIRFTARTVERLCDTLRAQV 345

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H Y+ IL RN+P+I
Sbjct: 346  DEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVTENHAYSAILSRNVPAI 405

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 406  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 465

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 466  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 525

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 526  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 585

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 586  HLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 645

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 646  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 681



 Score =  817 bits (2111), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/638 (65%), Positives = 509/638 (79%), Gaps = 19/638 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AF+   +  + EE+E  R K + LIKLGKERG+LT+ EIND 
Sbjct: 31  EKVKARDRRAKEKALLKDAFASS-QPGTVEELEERRSKLRALIKLGKERGFLTYGEINDH 89

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALST
Sbjct: 90  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALST 149

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 150 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 209

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNN-------------RVIKGNKNNNEEKILIESS 227
            A++++  EI+IDE+VDGLID N    +                +   +  EE+    ++
Sbjct: 210 MAERVANEEIRIDELVDGLIDTNAEDTDGFSEQEAEAIENEEEEEAEADEEEEEDDDGAA 269

Query: 228 SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
            A  +  QLE+LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRF
Sbjct: 270 QATANAAQLEELKRMSLEKFAMISEWFDKMRRAFEKEGYKSKSYLKAQETIQEELMMIRF 329

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D    
Sbjct: 330 TARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFIARFPGSETDLEWADKIVT 389

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
             H Y+ IL RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTE
Sbjct: 390 ENHAYSAILSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTE 449

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 450 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 509

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 510 SIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIA 569

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRM
Sbjct: 570 KEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 629

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 630 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>gi|387904766|ref|YP_006335104.1| RNA polymerase sigma factor RpoD [Burkholderia sp. KJ006]
 gi|387579658|gb|AFJ88373.1| RNA polymerase sigma factor RpoD [Burkholderia sp. KJ006]
          Length = 687

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/640 (65%), Positives = 508/640 (79%), Gaps = 22/640 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 48   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 106

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 107  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 166

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 167  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 226

Query: 987  DGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQ--------LEKL 1029
            DGL+D N         FS+       N++   E+   E    D             LE L
Sbjct: 227  DGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEAL 286

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            K  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTL
Sbjct: 287  KRASLEKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTL 346

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            R Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RN
Sbjct: 347  RAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRN 406

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            IP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKK
Sbjct: 407  IPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKK 466

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 467  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 526

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GD
Sbjct: 527  VHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGD 586

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 587  DDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTL 646

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 647  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 686



 Score =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 414/641 (64%), Positives = 509/641 (79%), Gaps = 23/641 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 33  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 91

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 92  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 151

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 152 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 211

Query: 182 ADKISKNEIKIDEIVDGLIDKN---------FSSNNRVIKGNKNNNEEKILIESSSADLS 232
           A++++  EI++DE+VDGL+D N         FS+       N++   E+   E    D  
Sbjct: 212 AERVANEEIRVDELVDGLLDPNAADAADTDGFSAKEAEAIENEDEEAEEEEEEEEEEDDD 271

Query: 233 TEQ--------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
                      LE LK  SL KFS IS  FDKMR+AFEKEGY S+SY+KA   I  E++ 
Sbjct: 272 GAAQATANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMT 331

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W + 
Sbjct: 332 IRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEK 391

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
                H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKRE
Sbjct: 392 IAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKRE 451

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           MTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 452 MTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 511

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIM
Sbjct: 512 ITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIM 571

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KV
Sbjct: 572 KIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKV 631

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 632 LRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 672


>gi|254184931|ref|ZP_04891520.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184215523|gb|EDU12504.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 680

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/636 (65%), Positives = 504/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 45   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 224  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 344  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAK LRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKTLRKLRHPSRSDKLKSFLEG 679



 Score =  818 bits (2112), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/639 (64%), Positives = 504/639 (78%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 207 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 266

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK LRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKTLRKLR 665


>gi|350545712|ref|ZP_08915172.1| RNA polymerase sigma factor RpoD [Candidatus Burkholderia kirkii
            UZHbot1]
 gi|350526502|emb|CCD40295.1| RNA polymerase sigma factor RpoD [Candidatus Burkholderia kirkii
            UZHbot1]
          Length = 680

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/632 (66%), Positives = 506/632 (80%), Gaps = 14/632 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 49   KDAFSSS-SPGTVEELEERRGKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 107

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 108  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 167

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A+++   E+++DE+V
Sbjct: 168  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVQNEEVRVDELV 227

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---LEKLKYESLIKF 1037
            DGLID N      FS        ++N   E+   E   +  ++     LE LK +SL KF
Sbjct: 228  DGLIDPNAEDTDGFSEQEAEAIESENEESEEEEEEDDGSAQASANAAQLEALKSQSLEKF 287

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + +S  FDKMR+A+EKEGY S++Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++V 
Sbjct: 288  ALVSEWFDKMRRAYEKEGYKSKAYLKAQEAIQTELMSIRFTARTVERLCDTLRAQVDEVR 347

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H+Y+ +L RNIP+I+E Q
Sbjct: 348  QVERQILHTVVDKCGMPRAEFITRFPGSETDLEWADKVVTEGHEYSAVLERNIPAIREQQ 407

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            Q+L++LQ  +VLPL DL++ NR+M AGE+K R+AKREMTEANLRLVISIAKKYT+RGLQF
Sbjct: 408  QRLLDLQARVVLPLKDLKETNRQMAAGELKTRQAKREMTEANLRLVISIAKKYTNRGLQF 467

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 468  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 527

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQILQETG EPDP  +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 528  KMNRISRQILQETGLEPDPVTLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 587

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFD
Sbjct: 588  FIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFD 647

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            VTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 648  VTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  817 bits (2111), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/634 (65%), Positives = 506/634 (79%), Gaps = 15/634 (2%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K K ++++ KE  LLK+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND 
Sbjct: 33  EKAKARDRRAKEKALLKDAFSSS-SPGTVEELEERRGKLRALIKLGKERGFLTYGEINDH 91

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALST
Sbjct: 92  LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALST 151

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 152 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 211

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSADLSTE 234
            A+++   E+++DE+VDGLID N      FS        ++N   E+   E   +  ++ 
Sbjct: 212 MAERVQNEEVRVDELVDGLIDPNAEDTDGFSEQEAEAIESENEESEEEEEEDDGSAQASA 271

Query: 235 Q---LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
               LE LK +SL KF+ +S  FDKMR+A+EKEGY S++Y+KA   I  E++ IRFTA++
Sbjct: 272 NAAQLEALKSQSLEKFALVSEWFDKMRRAYEKEGYKSKAYLKAQEAIQTELMSIRFTART 331

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H+
Sbjct: 332 VERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFITRFPGSETDLEWADKVVTEGHE 391

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+K R+AKREMTEANLR
Sbjct: 392 YSAVLERNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKTRQAKREMTEANLR 451

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 452 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 511

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG EPDP  +A KMEMPE+KIRKIMKIAKEP+
Sbjct: 512 QARTIRIPVHMIETINKMNRISRQILQETGLEPDPVTLAEKMEMPEDKIRKIMKIAKEPI 571

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGI
Sbjct: 572 SMETPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGI 631

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 632 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|78063051|ref|YP_372959.1| RNA polymerase sigma factor RpoD [Burkholderia sp. 383]
 gi|77970936|gb|ABB12315.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 808

 Score =  831 bits (2147), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 416/642 (64%), Positives = 510/642 (79%), Gaps = 24/642 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 167  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 225

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 226  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 285

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 286  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 345

Query: 987  DGLIDKNFSSN-------------------NRVIKGNKNNNEEKILIESSSADLSTEQLE 1027
            DGL+D N S +                       +  +   EE+    ++ A  +  QLE
Sbjct: 346  DGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEEEDDGAAQASANAAQLE 405

Query: 1028 KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 1087
             LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I  E++ IRFTA+++E+LCD
Sbjct: 406  ALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQTELMTIRFTARTVERLCD 465

Query: 1088 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILC 1147
            TLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L 
Sbjct: 466  TLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWSEKIMAEGHSYSAVLS 525

Query: 1148 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 1207
            RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIA
Sbjct: 526  RNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIA 585

Query: 1208 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 1267
            KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR
Sbjct: 586  KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 645

Query: 1268 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327
            IPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+
Sbjct: 646  IPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPI 705

Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387
            GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DH
Sbjct: 706  GDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDH 765

Query: 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 766  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 807



 Score =  819 bits (2115), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/643 (63%), Positives = 511/643 (79%), Gaps = 25/643 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 152 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 210

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 211 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 270

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 271 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 330

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSN-------------------NRVIKGNKNNNEEKI 222
           A++++  EI++DE+VDGL+D N S +                       +  +   EE+ 
Sbjct: 331 AERVANEEIRVDELVDGLLDPNASDSADTDGFSAKEAEAIENEDEEAEEEEEEEEEEEEE 390

Query: 223 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 282
              ++ A  +  QLE LK  SL KFS IS  FDKMR+AFEKEGY S++Y+KA   I  E+
Sbjct: 391 DDGAAQASANAAQLEALKRASLEKFSQISEWFDKMRRAFEKEGYKSKAYLKAQETIQTEL 450

Query: 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 342
           + IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W 
Sbjct: 451 MTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWS 510

Query: 343 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           +      H Y+ +L RN+P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AK
Sbjct: 511 EKIMAEGHSYSAVLSRNVPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAK 570

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           REMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 571 REMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 630

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRK
Sbjct: 631 QAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRK 690

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           IMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+
Sbjct: 691 IMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREA 750

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 751 KVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 793


>gi|395761653|ref|ZP_10442322.1| sigma 70 factor of RNA polymerase [Janthinobacterium lividum PAMC
            25724]
          Length = 849

 Score =  831 bits (2146), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/623 (65%), Positives = 494/623 (79%), Gaps = 19/623 (3%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S  ++E  RK+   LI +GKERG+LT++EIND LPE+IID E IE II TF  M I+V E
Sbjct: 226  SAADLERRRKQITGLINMGKERGFLTYAEINDQLPENIIDPEAIEGIIATFNDMGIAVYE 285

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D E+L+L++    +TSDD+VE A   ALSTVDSDFGRT DP++MYMREMG+V LLTR
Sbjct: 286  RAPDAESLLLTDNVATVTSDDEVEAAAATALSTVDSDFGRTTDPVRMYMREMGAVALLTR 345

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS- 996
            +GEIEIAKRIE GLKDMI AIS+CPTTI EI+  + KI+++EIK+DE+VDG +D N S+ 
Sbjct: 346  EGEIEIAKRIEGGLKDMIQAISACPTTIGEIVALSQKIARDEIKVDEVVDGFVDLNESNA 405

Query: 997  ------------NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHF 1044
                        +    +  +   EE       +A  S+EQL +LK  +L KF+ IS  +
Sbjct: 406  PAPAAAAAPVVASGDDEEEEEEAEEEDGDANGGAAGFSSEQLAQLKKNALEKFNVISTQY 465

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +KMRKA   EGYNS++Y KA   IS E+LGIRFTAK +EKLCDTLR Q+ +V  IE+ +L
Sbjct: 466  EKMRKA--PEGYNSKAYTKAQEAISQELLGIRFTAKVVEKLCDTLRGQMEEVRHIERAVL 523

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            E+ VNKCGMPR HFIKVFP NE +L WVD E   ++ Y+ IL RN+P++KELQ+K+I+LQ
Sbjct: 524  ELCVNKCGMPRAHFIKVFPGNECDLEWVDREVDCKYPYSAILSRNVPAVKELQKKMIDLQ 583

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
              + LPL DLR IN++M AGE +AR AKREMT ANLRLVISIAKKY +RGLQFLDLIQEG
Sbjct: 584  ARVALPLADLRKINKQMAAGEKRARHAKREMTVANLRLVISIAKKYINRGLQFLDLIQEG 643

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGL+KAVDKFEYRRGYKFSTYATWWIRQAITRSIAD ARTIR+PVHMIETINK++RISR
Sbjct: 644  NIGLLKAVDKFEYRRGYKFSTYATWWIRQAITRSIADMARTIRVPVHMIETINKMNRISR 703

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            QI+QETGSEPD + +A+KMEMPE K+R+IMKIAKEP+SME+P+G+D DS LGDFIED   
Sbjct: 704  QIMQETGSEPDLATLAVKMEMPENKVREIMKIAKEPISMETPMGEDGDSQLGDFIEDNTT 763

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
            LAP DAAL+ASMR+V+K++L+SLTPRE+KVLRMR+G+EMS+DHTLEEVGKQFDVTRERIR
Sbjct: 764  LAPLDAALHASMRNVIKEVLDSLTPREAKVLRMRYGVEMSNDHTLEEVGKQFDVTRERIR 823

Query: 1405 QIEAKALRKLRHPSRYYKLKIFL 1427
            QIEAKA+ KLR PSR  KLK FL
Sbjct: 824  QIEAKAMSKLRQPSRSDKLKTFL 846



 Score =  818 bits (2112), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/650 (62%), Positives = 502/650 (77%), Gaps = 23/650 (3%)

Query: 8   TKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPE 67
           +K +++K K  L   A +      S  ++E  RK+   LI +GKERG+LT++EIND LPE
Sbjct: 205 SKARDRKAKGGL---ADALGDPEASAADLERRRKQITGLINMGKERGFLTYAEINDQLPE 261

Query: 68  DIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDS 123
           +IID E IE II TF  M I+V E   D E+L+L++    +TSDD+VE A   ALSTVDS
Sbjct: 262 NIIDPEAIEGIIATFNDMGIAVYERAPDAESLLLTDNVATVTSDDEVEAAAATALSTVDS 321

Query: 124 DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 183
           DFGRT DP++MYMREMG+V LLTR+GEIEIAKRIE GLKDMI AIS+CPTTI EI+  + 
Sbjct: 322 DFGRTTDPVRMYMREMGAVALLTREGEIEIAKRIEGGLKDMIQAISACPTTIGEIVALSQ 381

Query: 184 KISKNEIKIDEIVDGLIDKNFSS-------------NNRVIKGNKNNNEEKILIESSSAD 230
           KI+++EIK+DE+VDG +D N S+             +    +  +   EE       +A 
Sbjct: 382 KIARDEIKVDEVVDGFVDLNESNAPAPAAAAAPVVASGDDEEEEEEAEEEDGDANGGAAG 441

Query: 231 LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
            S+EQL +LK  +L KF+ IS  ++KMRKA   EGYNS++Y KA   IS E+LGIRFTAK
Sbjct: 442 FSSEQLAQLKKNALEKFNVISTQYEKMRKA--PEGYNSKAYTKAQEAISQELLGIRFTAK 499

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
            +EKLCDTLR Q+ +V  IE+ +LE+ VNKCGMPR HFIKVFP NE +L WVD E   ++
Sbjct: 500 VVEKLCDTLRGQMEEVRHIERAVLELCVNKCGMPRAHFIKVFPGNECDLEWVDREVDCKY 559

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            Y+ IL RN+P++KELQ+K+I+LQ  + LPL DLR IN++M AGE +AR AKREMT ANL
Sbjct: 560 PYSAILSRNVPAVKELQKKMIDLQARVALPLADLRKINKQMAAGEKRARHAKREMTVANL 619

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKY +RGLQFLDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 620 RLVISIAKKYINRGLQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 679

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           D ARTIR+PVHMIETINK++RISRQI+QETGSEPD + +A+KMEMPE K+R+IMKIAKEP
Sbjct: 680 DMARTIRVPVHMIETINKMNRISRQIMQETGSEPDLATLAVKMEMPENKVREIMKIAKEP 739

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+G+D DS LGDFIED   LAP DAAL+ASMR+V+K++L+SLTPRE+KVLRMR+G
Sbjct: 740 ISMETPMGEDGDSQLGDFIEDNTTLAPLDAALHASMRNVIKEVLDSLTPREAKVLRMRYG 799

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWLEQRTHQN 639
           +EMS+DHTLEEVGKQFDVTRERIRQIEAKA+ KLR P   D L+    QN
Sbjct: 800 VEMSNDHTLEEVGKQFDVTRERIRQIEAKAMSKLRQPSRSDKLKTFLTQN 849


>gi|330821204|ref|YP_004350066.1| RpoD family RNA polymerase sigma-70 subunit [Burkholderia gladioli
            BSR3]
 gi|327373199|gb|AEA64554.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
            gladioli BSR3]
          Length = 805

 Score =  830 bits (2145), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/637 (65%), Positives = 509/637 (79%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+   +  + EE+E  R K + LIKLGK+RG+LT++EIND LP++  + E +E II 
Sbjct: 169  KEAFATS-QPGTAEELEERRVKLRALIKLGKDRGFLTYAEINDHLPDNFTETEALEGIIG 227

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 228  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 287

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++ +EI+IDE+V
Sbjct: 288  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANDEIRIDELV 347

Query: 987  DGLIDKNFSSNN--------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DGL D N    +                 +    + EE+    ++ A  +  QLE LK  
Sbjct: 348  DGLNDPNAEDADGFNAKEAEEAEQADEDEEEAAEDEEEEDDDGAAQATANAAQLEALKRT 407

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q
Sbjct: 408  SLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQ 467

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L W +      H Y+ IL RN+P+
Sbjct: 468  VDEVRQVERQILHIVVDKCGMPRSEFISRFPGSETDLAWAEKIATESHSYSAILQRNVPA 527

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 528  IHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 587

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 588  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 647

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 648  IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 707

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 708  SHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 767

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 768  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 804



 Score =  818 bits (2112), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/639 (64%), Positives = 510/639 (79%), Gaps = 20/639 (3%)

Query: 6   KKTKIKNKKTKETLL-KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +KTK ++++ KE LL K AF+   +  + EE+E  R K + LIKLGK+RG+LT++EIND 
Sbjct: 153 EKTKARDRRAKEKLLLKEAFATS-QPGTAEELEERRVKLRALIKLGKDRGFLTYAEINDH 211

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALST
Sbjct: 212 LPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALST 271

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL 
Sbjct: 272 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILA 331

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNN--------------RVIKGNKNNNEEKILIES 226
            A++++ +EI+IDE+VDGL D N    +                 +    + EE+    +
Sbjct: 332 MAERVANDEIRIDELVDGLNDPNAEDADGFNAKEAEEAEQADEDEEEAAEDEEEEDDDGA 391

Query: 227 SSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
           + A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 392 AQATANAAQLEALKRTSLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 451

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L W +   
Sbjct: 452 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFISRFPGSETDLAWAEKIA 511

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y+ IL RN+P+I E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 512 TESHSYSAILQRNVPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 571

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 572 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 631

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 632 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 691

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 692 AKEPISMETPIGDDDDSHLGDFIEDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 751

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 752 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|167724581|ref|ZP_02407817.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 680

 Score =  830 bits (2145), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/636 (65%), Positives = 504/636 (79%), Gaps = 18/636 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 45   KEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 103

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 104  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 163

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E ++DE+V
Sbjct: 164  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRVDELV 223

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ-------------LEKLKYES 1033
            DGLID N +  +   + +    E +        +   E              LE LK  S
Sbjct: 224  DGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGAAQATANAAQLEALKRAS 283

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+
Sbjct: 284  LEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIRFTARTVERLCDTLRAQV 343

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y  IL RNIP+I
Sbjct: 344  DEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYGAILSRNIPAI 403

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+R
Sbjct: 404  REQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNR 463

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 464  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 523

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DS
Sbjct: 524  ETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDS 583

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTP E+KVLRMRFGIEMS+DHTLEEVG
Sbjct: 584  HLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPSEAKVLRMRFGIEMSTDHTLEEVG 643

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 644  KQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 679



 Score =  817 bits (2110), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/639 (64%), Positives = 504/639 (78%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K ++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND
Sbjct: 28  GEKAKARDRRAKEKALLKEAFATSTPGTA-EELEERRTKLRALIKLGKERGFLTYAEIND 86

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LP++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALS
Sbjct: 87  HLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALS 146

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL
Sbjct: 147 TVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADIL 206

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ---- 235
             A++++  E ++DE+VDGLID N +  +   + +    E +        +   E     
Sbjct: 207 AMAERVANEESRVDELVDGLIDPNAADTDGFSEKDAEEIENEDAEAEEDDEEEEEDDDGA 266

Query: 236 ---------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                    LE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I NE++ IR
Sbjct: 267 AQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKSYLKAQETIQNELMSIR 326

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +   
Sbjct: 327 FTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVA 386

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H Y  IL RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 387 AEGHSYGAILSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 446

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 447 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 506

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 507 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 566

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTP E+KVLR
Sbjct: 567 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPSEAKVLR 626

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|73540591|ref|YP_295111.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha JMP134]
 gi|72118004|gb|AAZ60267.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia eutropha JMP134]
          Length = 783

 Score =  830 bits (2145), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/628 (65%), Positives = 507/628 (80%), Gaps = 17/628 (2%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T   + I+
Sbjct: 155  QQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 214

Query: 879  VSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 215  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 274

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL  A++++ +EIKIDE VDGLID N 
Sbjct: 275  LTREGEIVIAKRIEAGLKDMVMAISACPVTISEILANAERVASDEIKIDEFVDGLIDPNA 334

Query: 995  -------------SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNIS 1041
                            +     ++ ++E++   +++ A  S  QLE+LK  +L KF  I+
Sbjct: 335  DEMAQEAAGASAADEEDLESDEDEESDEDEEDDDAAGAGASARQLEELKLSALEKFRVIA 394

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              FDKMR+AFEKEGYNS+ Y+KA   I  E++GIRFTA+S+E+LCDTLR Q+++V ++E+
Sbjct: 395  EQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIRFTARSVERLCDTLRGQVDEVRKLER 454

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
             IL IVV+KCGMPR  F+  FP NE NL+WV         Y+ I+ RN+P++ ELQQKLI
Sbjct: 455  SILNIVVDKCGMPRSDFVARFPGNETNLDWVGTIVADGKPYSTIVERNVPAVHELQQKLI 514

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
            +LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 515  DLQSRVVLPLKELKGVNRKMAEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLI 574

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 575  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNR 634

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED
Sbjct: 635  ISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIED 694

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
             N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRE
Sbjct: 695  TNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRE 754

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            RIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 755  RIRQIEAKALRKLRHPSRSDKLKSFLEG 782



 Score =  816 bits (2107), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/638 (64%), Positives = 508/638 (79%), Gaps = 18/638 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   +  + EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 132 TEKQKAKDRKAKEKALLKEFA-STQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDH 190

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 191 LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 250

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 251 VDSEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEAGLKDMVMAISACPVTISEILA 310

Query: 181 AADKISKNEIKIDEIVDGLIDKNF-------------SSNNRVIKGNKNNNEEKILIESS 227
            A++++ +EIKIDE VDGLID N                 +     ++ ++E++   +++
Sbjct: 311 NAERVASDEIKIDEFVDGLIDPNADEMAQEAAGASAADEEDLESDEDEESDEDEEDDDAA 370

Query: 228 SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
            A  S  QLE+LK  +L KF  I+  FDKMR+AFEKEGYNS+ Y+KA   I  E++GIRF
Sbjct: 371 GAGASARQLEELKLSALEKFRVIAEQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIRF 430

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+S+E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL+WV     
Sbjct: 431 TARSVERLCDTLRGQVDEVRKLERSILNIVVDKCGMPRSDFVARFPGNETNLDWVGTIVA 490

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
               Y+ I+ RN+P++ ELQQKLI+LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMTE
Sbjct: 491 DGKPYSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKGVNRKMAEGEKRAREAKREMTE 550

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 551 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 610

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 611 SIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIA 670

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRM
Sbjct: 671 KEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRM 730

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 731 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 768


>gi|421748390|ref|ZP_16185994.1| RNA polymerase sigma factor RpoD [Cupriavidus necator HPC(L)]
 gi|409772891|gb|EKN54797.1| RNA polymerase sigma factor RpoD [Cupriavidus necator HPC(L)]
          Length = 750

 Score =  830 bits (2144), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/630 (65%), Positives = 505/630 (80%), Gaps = 19/630 (3%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T   + I+
Sbjct: 120  QQGTEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 179

Query: 879  VSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 180  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 239

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  A++++ +EIKIDE VDGLID N 
Sbjct: 240  LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVDGLIDPNA 299

Query: 995  SSNNRVI---------------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSN 1039
                  +               + +    +E+   +++    S  QLE+LK  +L KF  
Sbjct: 300  EEAVEEVGVTPAAAAASDDEELESDDEEADEEDDDDAAGGGASARQLEELKVAALEKFRV 359

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            I+  FDKMR+AFEKEGY S+ YIKA   I NE++GIRFTA+++E+LCDTLR Q+++V ++
Sbjct: 360  IADQFDKMRRAFEKEGYKSKPYIKAQEAIQNELMGIRFTARNVERLCDTLRGQVDEVRKL 419

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ IL IVV+KCGMPR  F+  FP NE NL+W+         Y+ I+ RN+P++ ELQQK
Sbjct: 420  ERAILNIVVDKCGMPRADFVARFPGNETNLDWIHTVVADNKPYSTIVERNVPAVHELQQK 479

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            LI+LQ  +VLPL +L+++NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLD
Sbjct: 480  LIDLQARVVLPLKELKEVNRKMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLD 539

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 540  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 599

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 600  NRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 659

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVT
Sbjct: 660  EDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVT 719

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            RERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 720  RERIRQIEAKALRKLRHPSRSDKLKSFLEG 749



 Score =  816 bits (2107), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/640 (63%), Positives = 506/640 (79%), Gaps = 20/640 (3%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   +  + EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 97  TEKQKAKDRKAKEKALLKEFA-SAQQGTEEELEARRQKLKALIKLGKSRGYLTYAEINDH 155

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 156 LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 215

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 216 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 275

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVI---------------KGNKNNNEEKILIE 225
            A++++ +EIKIDE VDGLID N       +               + +    +E+   +
Sbjct: 276 HAERVANDEIKIDEFVDGLIDPNAEEAVEEVGVTPAAAAASDDEELESDDEEADEEDDDD 335

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++    S  QLE+LK  +L KF  I+  FDKMR+AFEKEGY S+ YIKA   I NE++GI
Sbjct: 336 AAGGGASARQLEELKVAALEKFRVIADQFDKMRRAFEKEGYKSKPYIKAQEAIQNELMGI 395

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL+W+   
Sbjct: 396 RFTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVARFPGNETNLDWIHTV 455

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
                 Y+ I+ RN+P++ ELQQKLI+LQ  +VLPL +L+++NRKM  GE +AR+AKREM
Sbjct: 456 VADNKPYSTIVERNVPAVHELQQKLIDLQARVVLPLKELKEVNRKMSEGEKRAREAKREM 515

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 516 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 575

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 576 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMK 635

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVL
Sbjct: 636 IAKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVL 695

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 696 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 735


>gi|167583913|ref|ZP_02376301.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ubonensis Bu]
          Length = 681

 Score =  830 bits (2144), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/639 (65%), Positives = 509/639 (79%), Gaps = 21/639 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 43   KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 101

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 102  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 161

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  E +IDE+V
Sbjct: 162  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEESRIDELV 221

Query: 987  DGLIDKNFSSNN----------------RVIKGNKNNNEEKILIESSSADLSTEQLEKLK 1030
            DGL+D N S  +                   +  +   EE+    ++ A  +  QLE LK
Sbjct: 222  DGLLDPNASDTDTDGFSAKAAEEIENEDDEAEEEEEEEEEEDDDGAAQATANAAQLEALK 281

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
              SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR
Sbjct: 282  RASLEKFAQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTLR 341

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
             Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RNI
Sbjct: 342  AQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKVAAEGHSYSAVLSRNI 401

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKY
Sbjct: 402  PAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKY 461

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 462  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 521

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD
Sbjct: 522  HMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDD 581

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            +DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLE
Sbjct: 582  DDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLE 641

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            EVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 642  EVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 680



 Score =  818 bits (2113), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/640 (64%), Positives = 510/640 (79%), Gaps = 22/640 (3%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 28  KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 86

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 87  PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 146

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 147 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 206

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNN----------------RVIKGNKNNNEEKILIE 225
           A++++  E +IDE+VDGL+D N S  +                   +  +   EE+    
Sbjct: 207 AERVANEESRIDELVDGLLDPNASDTDTDGFSAKAAEEIENEDDEAEEEEEEEEEEDDDG 266

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           ++ A  +  QLE LK  SL KF+ IS  FDKMR+AFEKEGY S+SY+KA   I  E++ I
Sbjct: 267 AAQATANAAQLEALKRASLEKFAQISEWFDKMRRAFEKEGYKSKSYLKAQETIQTELMTI 326

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +  
Sbjct: 327 RFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKV 386

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
               H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREM
Sbjct: 387 AAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREM 446

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
           TEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 447 TEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 506

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMK
Sbjct: 507 TRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMK 566

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVL
Sbjct: 567 IAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 626

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 627 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|377813351|ref|YP_005042600.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. YI23]
 gi|357938155|gb|AET91713.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. YI23]
          Length = 737

 Score =  829 bits (2141), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 419/637 (65%), Positives = 507/637 (79%), Gaps = 19/637 (2%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND LP++  + E IE II 
Sbjct: 101  KDAFSSS-APGTVEELEERRGKLRALIKLGKERGFLTYGEINDHLPDNFTETEAIEGIIS 159

Query: 871  TFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 160  TFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 219

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL  A+++   E+++DE+V
Sbjct: 220  REMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILAMAERVQNEEVRVDELV 279

Query: 987  DGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYE 1032
            DGLID N      FS        ++    E+   E    +         +  QLE LK +
Sbjct: 280  DGLIDPNAQDTDGFSEQEAEAIESEEEETEEEGDEEEEEEDDGSAQASANAAQLEALKLQ 339

Query: 1033 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            SL KF+ IS  F+KMR+A+EKEGY S++Y+KA   I  E++ IRFTA+++E+LCDTLR Q
Sbjct: 340  SLEKFALISEWFEKMRRAYEKEGYKSKAYLKAQEAIQTELMNIRFTARTVERLCDTLRAQ 399

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D      H+Y+ +L RNIP+
Sbjct: 400  VDEVRQVERQILHTVVDKCGMPRAEFITRFPGSETDLEWADKVVAEGHEYSAVLERNIPA 459

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 460  IREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 519

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 520  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 579

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 580  IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 639

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 640  SHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 699

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 700  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 736



 Score =  815 bits (2104), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/639 (64%), Positives = 507/639 (79%), Gaps = 20/639 (3%)

Query: 6   KKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +K + ++++ KE  LLK+AFS      + EE+E  R K + LIKLGKERG+LT+ EIND 
Sbjct: 85  EKARARDRRAKEKALLKDAFSSS-APGTVEELEERRGKLRALIKLGKERGFLTYGEINDH 143

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALST 120
           LP++  + E IE II TF  M ++V E   D ETL+L+    N +SDD+VEE  E ALST
Sbjct: 144 LPDNFTETEAIEGIISTFNDMGVAVYEQAPDAETLLLNDNAPNASSDDEVEEEAEVALST 203

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GLK M+ AIS+CPTTI +IL 
Sbjct: 204 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLKHMVMAISACPTTIADILA 263

Query: 181 AADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKGNKNNNEEKILIESSSAD---- 230
            A+++   E+++DE+VDGLID N      FS        ++    E+   E    +    
Sbjct: 264 MAERVQNEEVRVDELVDGLIDPNAQDTDGFSEQEAEAIESEEEETEEEGDEEEEEEDDGS 323

Query: 231 ----LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                +  QLE LK +SL KF+ IS  F+KMR+A+EKEGY S++Y+KA   I  E++ IR
Sbjct: 324 AQASANAAQLEALKLQSLEKFALISEWFEKMRRAYEKEGYKSKAYLKAQEAIQTELMNIR 383

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V Q+E+QIL  VV+KCGMPR  FI  FP +E +L W D   
Sbjct: 384 FTARTVERLCDTLRAQVDEVRQVERQILHTVVDKCGMPRAEFITRFPGSETDLEWADKVV 443

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
              H+Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMT
Sbjct: 444 AEGHEYSAVLERNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMT 503

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 504 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 563

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 564 RSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKI 623

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N +APSDAAL+ASMR VVKD+L+SLTPRE+KVLR
Sbjct: 624 AKEPISMETPIGDDDDSHLGDFIEDTNTVAPSDAALHASMRDVVKDVLDSLTPREAKVLR 683

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 684 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 722


>gi|17546934|ref|NP_520336.1| RNA polymerase sigma factor RpoD [Ralstonia solanacearum GMI1000]
 gi|17429234|emb|CAD15922.1| probable rna polymerase sigma d (sigma-70) factor transcription
            regulator protein [Ralstonia solanacearum GMI1000]
          Length = 755

 Score =  826 bits (2134), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/633 (64%), Positives = 505/633 (79%), Gaps = 17/633 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 122  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 181

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 182  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 241

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 242  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 301

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSAD-------------LSTEQLEKLKYESLIK 1036
            ID N  +      G+++ + E    + S  +              S  QLE+LK  +L K
Sbjct: 302  IDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLEELKQAALAK 361

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA+++E+LCDTLR Q+++V
Sbjct: 362  FAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEV 421

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ EL
Sbjct: 422  RKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHEL 481

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            QQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQ
Sbjct: 482  QQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQ 541

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 542  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 601

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 602  NKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 661

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQF
Sbjct: 662  DFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQF 721

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            DVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 722  DVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 754



 Score =  812 bits (2098), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/636 (63%), Positives = 503/636 (79%), Gaps = 17/636 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 105 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 164

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 165 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 224

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 225 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 284

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD------------ 230
           ++++ +E KIDE +DGLID N  +      G+++ + E    + S  +            
Sbjct: 285 ERVANDEAKIDEYIDGLIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSS 344

Query: 231 -LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTA 289
             S  QLE+LK  +L KF+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA
Sbjct: 345 AASARQLEELKQAALAKFAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTA 404

Query: 290 KSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ 349
           +++E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++      
Sbjct: 405 RNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADG 464

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEAN
Sbjct: 465 KPYSAIVERNIPAVHELQQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEAN 524

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 525 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 584

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKE
Sbjct: 585 ADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKE 644

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRF
Sbjct: 645 PISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRF 704

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 705 GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>gi|421891293|ref|ZP_16322102.1| RNA polymerase sigma70 factor [Ralstonia solanacearum K60-1]
 gi|378963336|emb|CCF98850.1| RNA polymerase sigma70 factor [Ralstonia solanacearum K60-1]
          Length = 666

 Score =  825 bits (2131), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/631 (64%), Positives = 502/631 (79%), Gaps = 15/631 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 35   FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 94

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 95   DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 154

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 155  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 214

Query: 990  IDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            ID N  +  +                    E +    +  +  S  QLE+LK  +L KFS
Sbjct: 215  IDPNAEAEAQSADEDEDFEDEEADEGDEEEEGEDDDGAGGSAASARQLEELKQAALEKFS 274

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA+++E+LCDTLR Q+++V +
Sbjct: 275  IIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRK 334

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQ
Sbjct: 335  LERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQ 394

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFL
Sbjct: 395  KLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFL 454

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 455  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 514

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 515  MNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDF 574

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDV
Sbjct: 575  IEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDV 634

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            TRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 635  TRERIRQIEAKALRKLRHPSRSDKLKSFLEG 665



 Score =  811 bits (2096), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/634 (63%), Positives = 500/634 (78%), Gaps = 15/634 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 18  KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 77

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 78  DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 137

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 138 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 197

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADL 231
           ++++ +E KIDE +DGLID N  +  +                    E +    +  +  
Sbjct: 198 ERVANDEAKIDEYIDGLIDPNAEAEAQSADEDEDFEDEEADEGDEEEEGEDDDGAGGSAA 257

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           S  QLE+LK  +L KFS I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA++
Sbjct: 258 SARQLEELKQAALEKFSIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARN 317

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++        
Sbjct: 318 VERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP 377

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ I+ RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLR
Sbjct: 378 YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLR 437

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 438 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 497

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+
Sbjct: 498 QARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPI 557

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGI
Sbjct: 558 SMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGI 617

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 618 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 651


>gi|344167290|emb|CCA79498.1| RNA polymerase sigma70 factor [blood disease bacterium R229]
          Length = 679

 Score =  825 bits (2130), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/627 (65%), Positives = 503/627 (80%), Gaps = 11/627 (1%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 35   FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 94

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 95   DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 154

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 155  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 214

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADL-------STEQLEKLKYESLIKFSNISF 1042
            ID N  +          + E++   E    D        S  QL++LK  +LI+F  I  
Sbjct: 215  IDPNAEAEAAAQAEEDEDFEDEEAEEEDEDDEGAGAAAASARQLDELKQAALIRFGVIGE 274

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             F+KMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+LCDTLR Q+++V ++E+ 
Sbjct: 275  QFEKMRRAFEKEGYKSKPYVKAQEAIQAELMCIRFTARNVERLCDTLRGQVDEVRKLERA 334

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            IL IVV+KCGMPR  F+  FP NE NL W+D        Y+ I+ RNIP++ ELQQKLI+
Sbjct: 335  ILNIVVDKCGMPRGDFVSRFPGNETNLKWIDTVIADGKPYSAIVERNIPAVHELQQKLID 394

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 395  LQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQ 454

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 455  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRI 514

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED 
Sbjct: 515  SRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDT 574

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
            N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRER
Sbjct: 575  NTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRER 634

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            IRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 635  IRQIEAKALRKLRHPSRSDKLKSFLEG 661



 Score =  811 bits (2096), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/630 (63%), Positives = 501/630 (79%), Gaps = 11/630 (1%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 18  KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 77

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 78  DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 137

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 138 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 197

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL-------STEQ 235
           ++++ +E KIDE +DGLID N  +          + E++   E    D        S  Q
Sbjct: 198 ERVANDEAKIDEYIDGLIDPNAEAEAAAQAEEDEDFEDEEAEEEDEDDEGAGAAAASARQ 257

Query: 236 LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKL 295
           L++LK  +LI+F  I   F+KMR+AFEKEGY S+ Y+KA   I  E++ IRFTA+++E+L
Sbjct: 258 LDELKQAALIRFGVIGEQFEKMRRAFEKEGYKSKPYVKAQEAIQAELMCIRFTARNVERL 317

Query: 296 CDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLI 355
           CDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+D        Y+ I
Sbjct: 318 CDTLRGQVDEVRKLERAILNIVVDKCGMPRGDFVSRFPGNETNLKWIDTVIADGKPYSAI 377

Query: 356 LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
           + RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVIS
Sbjct: 378 VERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVIS 437

Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
           IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 438 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 497

Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535
           IRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+
Sbjct: 498 IRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMET 557

Query: 536 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 595
           P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+
Sbjct: 558 PIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMST 617

Query: 596 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 618 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 647


>gi|156563504|dbj|BAF76047.1| Sigma70 [Ralstonia solanacearum]
          Length = 755

 Score =  824 bits (2129), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/633 (64%), Positives = 504/633 (79%), Gaps = 17/633 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 122  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 181

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 182  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 241

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 242  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 301

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSAD-------------LSTEQLEKLKYESLIK 1036
            ID N  +      G+++ + E    + S  +              S  QLE+LK  +L K
Sbjct: 302  IDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLEELKQAALAK 361

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA+++E+LCDTLR Q+++V
Sbjct: 362  FAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEV 421

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ EL
Sbjct: 422  RKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHEL 481

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            QQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQ
Sbjct: 482  QQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQ 541

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 542  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 601

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 602  NKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 661

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N LAP++AAL+ SMR VVKD+L+SL PRE+KVLRMRFGIEMS+DHTLEEVGKQF
Sbjct: 662  DFIEDTNTLAPAEAALHGSMRGVVKDVLDSLAPREAKVLRMRFGIEMSTDHTLEEVGKQF 721

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            DVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 722  DVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 754



 Score =  811 bits (2094), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/636 (63%), Positives = 502/636 (78%), Gaps = 17/636 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 105 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 164

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 165 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 224

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 225 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 284

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD------------ 230
           ++++ +E KIDE +DGLID N  +      G+++ + E    + S  +            
Sbjct: 285 ERVANDEAKIDEYIDGLIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSS 344

Query: 231 -LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTA 289
             S  QLE+LK  +L KF+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA
Sbjct: 345 AASARQLEELKQAALAKFAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTA 404

Query: 290 KSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ 349
           +++E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++      
Sbjct: 405 RNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADG 464

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEAN
Sbjct: 465 KPYSAIVERNIPAVHELQQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEAN 524

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 525 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 584

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKE
Sbjct: 585 ADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKE 644

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SL PRE+KVLRMRF
Sbjct: 645 PISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLAPREAKVLRMRF 704

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 705 GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>gi|206562773|ref|YP_002233536.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
 gi|198038813|emb|CAR54775.1| RNA polymerase sigma factor RpoD [Burkholderia cenocepacia J2315]
          Length = 621

 Score =  824 bits (2129), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/619 (66%), Positives = 501/619 (80%), Gaps = 21/619 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            K + LIKLGKERG+LT++EIND LP++  + E +E II TF  M ++V E   D ETL+L
Sbjct: 2    KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 892  SN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++     +SDD+VEE  E ALSTVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRI
Sbjct: 62   NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNN 998
            E+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+VDGL+D N         FS+  
Sbjct: 122  EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLLDPNAADAADTDGFSAKE 181

Query: 999  RVIKGNKNNNEEKILIESSSADLS--------TEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                 N++   E+   E    +            QLE LK  SL KFS IS  FDKMR+A
Sbjct: 182  AEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEALKRASLEKFSQISEWFDKMRRA 241

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            FEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+K
Sbjct: 242  FEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDK 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            CGMPR  FI  FP NE +L+W +  T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLP
Sbjct: 302  CGMPRSEFIARFPGNETDLDWAEKITAEGHSYSAVLSRNVPAIREQQQRLLDLQARVVLP 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  LKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DA
Sbjct: 482  GLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADA 541

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            AL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542  ALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 1411 LRKLRHPSRYYKLKIFLEG 1429
            LRKLRHPSR  KLK FLEG
Sbjct: 602  LRKLRHPSRSDKLKSFLEG 620



 Score =  803 bits (2073), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/605 (66%), Positives = 490/605 (80%), Gaps = 21/605 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           K + LIKLGKERG+LT++EIND LP++  + E +E II TF  M ++V E   D ETL+L
Sbjct: 2   KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 102 SN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++     +SDD+VEE  E ALSTVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRI
Sbjct: 62  NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNN 208
           E+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+VDGL+D N         FS+  
Sbjct: 122 EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLLDPNAADAADTDGFSAKE 181

Query: 209 RVIKGNKNNNEEKILIESSSADLS--------TEQLEKLKYESLIKFSNISFHFDKMRKA 260
                N++   E+   E    +            QLE LK  SL KFS IS  FDKMR+A
Sbjct: 182 AEAIENEDEEAEEEEEEEEEEEDDGAAQASANAAQLEALKRASLEKFSQISEWFDKMRRA 241

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           FEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+K
Sbjct: 242 FEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDK 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
           CGMPR  FI  FP NE +L+W +  T   H Y+ +L RN+P+I+E QQ+L++LQ  +VLP
Sbjct: 302 CGMPRSEFIARFPGNETDLDWAEKITAEGHSYSAVLSRNVPAIREQQQRLLDLQARVVLP 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 LKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DA
Sbjct: 482 GLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADA 541

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           AL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542 ALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 621 LRKLR 625
           LRKLR
Sbjct: 602 LRKLR 606


>gi|194290318|ref|YP_002006225.1| RNA polymerase sigma factor rpod [Cupriavidus taiwanensis LMG 19424]
 gi|193224153|emb|CAQ70162.1| RNA POLYMERASE SIGMA D (SIGMA-70) FACTOR TRANSCRIPTION REGULATOR
            PROTEIN [Cupriavidus taiwanensis LMG 19424]
          Length = 683

 Score =  824 bits (2129), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/629 (65%), Positives = 498/629 (79%), Gaps = 18/629 (2%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T   + I+
Sbjct: 54   QQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 113

Query: 879  VSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 114  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 173

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  A++++ +EIKIDE VDGLID N 
Sbjct: 174  LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVDGLIDPNA 233

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLST--------------EQLEKLKYESLIKFSNI 1040
                          +++ L      +                  QLE+LK  +L KF  I
Sbjct: 234  EEAPEAPSAPAAAADDEDLESDDDEEGDEDEDDEGGAGAGASARQLEELKQNALEKFRVI 293

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            +  FDKMR+AFEKEGY S+ Y+KA   I  E++GIRFTA+++E+LCDTLR Q+++V ++E
Sbjct: 294  AEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMGIRFTARNVERLCDTLRGQVDEVRKLE 353

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + IL IVV+KCGMPR  F+  FP NE NL W+         Y+ I+ RN+P++ ELQQKL
Sbjct: 354  RAILNIVVDKCGMPRADFVARFPGNETNLEWIHTVVADGKGYSTIVERNVPAVHELQQKL 413

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            I+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDL
Sbjct: 414  IDLQARVVLPLKELKDVNRKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDL 473

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 474  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 533

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 534  RISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIE 593

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTR
Sbjct: 594  DTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTR 653

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            ERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 654  ERIRQIEAKALRKLRHPSRSDKLKSFLEG 682



 Score =  810 bits (2093), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 407/639 (63%), Positives = 499/639 (78%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   +  + EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 31  TEKQKAKDRKAKEKALLKEFA-STQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDH 89

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 90  LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 149

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 150 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 209

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLST------- 233
            A++++ +EIKIDE VDGLID N               +++ L      +          
Sbjct: 210 HAERVANDEIKIDEFVDGLIDPNAEEAPEAPSAPAAAADDEDLESDDDEEGDEDEDDEGG 269

Query: 234 -------EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                   QLE+LK  +L KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++GIR
Sbjct: 270 AGAGASARQLEELKQNALEKFRVIAEQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMGIR 329

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V ++E+ IL IVV+KCGMPR  F+  FP NE NL W+    
Sbjct: 330 FTARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMPRADFVARFPGNETNLEWIHTVV 389

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
                Y+ I+ RN+P++ ELQQKLI+LQ  +VLPL +L+D+NRKM  GE +AR+AKREMT
Sbjct: 390 ADGKGYSTIVERNVPAVHELQQKLIDLQARVVLPLKELKDVNRKMSEGERRAREAKREMT 449

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 450 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 509

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 510 RSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKI 569

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLR
Sbjct: 570 AKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLR 629

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 630 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|339326725|ref|YP_004686418.1| DNA-directed RNA polymerase sigma subunit RpoD [Cupriavidus necator
            N-1]
 gi|338166882|gb|AEI77937.1| DNA-directed RNA polymerase sigma subunit RpoD [Cupriavidus necator
            N-1]
          Length = 684

 Score =  823 bits (2125), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/629 (65%), Positives = 497/629 (79%), Gaps = 18/629 (2%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E I++++ T   + I+
Sbjct: 55   QQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDSETIDTLVATLNDIGIA 114

Query: 879  VSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L++     TS+++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 115  VYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 174

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  A++++ +EIKIDE VDGLID N 
Sbjct: 175  LTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAHAERVANDEIKIDEFVDGLIDPNA 234

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLST--------------EQLEKLKYESLIKFSNI 1040
                           E+ L      D                  QLE+LK  +L KF  I
Sbjct: 235  EEVAESPAAAAAPAAEEDLESDDEEDADEDEDDEGGAGAGASARQLEELKQNALEKFRVI 294

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            +  FDKMR+AFEKEGYNS+ Y+KA   I  E++GIRFTA+++E+LCDTLR Q+++V ++E
Sbjct: 295  AEQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIRFTARNVERLCDTLRGQVDEVRKLE 354

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + IL  +V+KCGMPR  F+  FP NE NL WV         Y+ I+ RN+P++ ELQQKL
Sbjct: 355  RAILNTIVDKCGMPRAEFVARFPGNETNLEWVHTIVADGKPYSTIVERNVPAVHELQQKL 414

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            I+LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDL
Sbjct: 415  IDLQSRVVLPLKELKGVNRKMAEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDL 474

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 475  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 534

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 535  RISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIE 594

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTR
Sbjct: 595  DTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTR 654

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            ERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 655  ERIRQIEAKALRKLRHPSRSDKLKSFLEG 683



 Score =  809 bits (2089), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 408/639 (63%), Positives = 498/639 (77%), Gaps = 19/639 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
            +K K K++K KE  L   F+   +  + EE+E  R+K K LIKLGK RGYLT++EIND 
Sbjct: 32  TEKQKAKDRKAKEKALLKEFA-STQQGTEEELELRRQKLKALIKLGKSRGYLTYAEINDH 90

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALST 120
           LP+D++D E I++++ T   + I+V E   D ETL+L++     TS+++ EE  EAALST
Sbjct: 91  LPDDMVDSETIDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSATSEEEAEEEAEAALST 150

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL 
Sbjct: 151 VDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILA 210

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLST------- 233
            A++++ +EIKIDE VDGLID N                E+ L      D          
Sbjct: 211 HAERVANDEIKIDEFVDGLIDPNAEEVAESPAAAAAPAAEEDLESDDEEDADEDEDDEGG 270

Query: 234 -------EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIR 286
                   QLE+LK  +L KF  I+  FDKMR+AFEKEGYNS+ Y+KA   I  E++GIR
Sbjct: 271 AGAGASARQLEELKQNALEKFRVIAEQFDKMRRAFEKEGYNSKPYVKAQEAIQAELMGIR 330

Query: 287 FTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNET 346
           FTA+++E+LCDTLR Q+++V ++E+ IL  +V+KCGMPR  F+  FP NE NL WV    
Sbjct: 331 FTARNVERLCDTLRGQVDEVRKLERAILNTIVDKCGMPRAEFVARFPGNETNLEWVHTIV 390

Query: 347 KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMT 406
                Y+ I+ RN+P++ ELQQKLI+LQ+ +VLPL +L+ +NRKM  GE +AR+AKREMT
Sbjct: 391 ADGKPYSTIVERNVPAVHELQQKLIDLQSRVVLPLKELKGVNRKMAEGERRAREAKREMT 450

Query: 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466
           EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT
Sbjct: 451 EANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 510

Query: 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 526
           RSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKI
Sbjct: 511 RSIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKI 570

Query: 527 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLR 586
           AKEP+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLR
Sbjct: 571 AKEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRDVVKDVLDSLTPREAKVLR 630

Query: 587 MRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           MRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 631 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 669


>gi|4128212|gb|AAD03549.1| principal sigma factor [Burkholderia cepacia]
          Length = 621

 Score =  821 bits (2121), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/619 (66%), Positives = 498/619 (80%), Gaps = 21/619 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            K + LIKLGKERG+LT++EIND LP++  + E +E II TF  M ++V E   D ETL+L
Sbjct: 2    KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 892  SN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++     +SDD+VEE  E ALSTVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRI
Sbjct: 62   NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNN 998
            E+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+VDGL+D N         FS+  
Sbjct: 122  EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLLDPNAADAADTDGFSAKE 181

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQ--------LEKLKYESLIKFSNISFHFDKMRKA 1050
                 N++   E+   E    D             LE LK  SL KFS IS  FDKMR+A
Sbjct: 182  AEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEALKRASLEKFSQISEWFDKMRRA 241

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            FEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+K
Sbjct: 242  FEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDK 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            CGMPR  FI  FP +E +L+W +      H Y+ +L RNIP+I+E QQ+L++LQ  +VLP
Sbjct: 302  CGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLP 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  LKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DA
Sbjct: 482  GLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADA 541

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            AL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542  ALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 1411 LRKLRHPSRYYKLKIFLEG 1429
            LRKLRHPSR  KLK FLEG
Sbjct: 602  LRKLRHPSRSDKLKSFLEG 620



 Score =  800 bits (2065), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/605 (66%), Positives = 487/605 (80%), Gaps = 21/605 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           K + LIKLGKERG+LT++EIND LP++  + E +E II TF  M ++V E   D ETL+L
Sbjct: 2   KLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLL 61

Query: 102 SN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++     +SDD+VEE  E ALSTVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRI
Sbjct: 62  NDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRI 121

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNN 208
           E+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+VDGL+D N         FS+  
Sbjct: 122 EDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELVDGLLDPNAADAADTDGFSAKE 181

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQ--------LEKLKYESLIKFSNISFHFDKMRKA 260
                N++   E+   E    D             LE LK  SL KFS IS  FDKMR+A
Sbjct: 182 AEAIENEDEEAEEEEEEEEEEDDDGAAQATANAAQLEALKRASLEKFSQISEWFDKMRRA 241

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           FEKEGY S+SY+KA   I  E++ IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+K
Sbjct: 242 FEKEGYKSKSYLKAQETIQTELMTIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDK 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
           CGMPR  FI  FP +E +L+W +      H Y+ +L RNIP+I+E QQ+L++LQ  +VLP
Sbjct: 302 CGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRNIPAIREQQQRLLDLQARVVLP 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 LKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DA
Sbjct: 482 GLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTVAPADA 541

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           AL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542 ALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 621 LRKLR 625
           LRKLR
Sbjct: 602 LRKLR 606


>gi|393778030|ref|ZP_10366313.1| RNA polymerase sigma factor RpoD [Ralstonia sp. PBA]
 gi|392714916|gb|EIZ02507.1| RNA polymerase sigma factor RpoD [Ralstonia sp. PBA]
          Length = 859

 Score =  820 bits (2119), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/629 (64%), Positives = 498/629 (79%), Gaps = 19/629 (3%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +  + EE+E  R+K K +IKLGK RGYLT++EIND LP+D+++ + +++++ T   + I+
Sbjct: 229  QPGTEEELELRRQKLKAVIKLGKSRGYLTYAEINDHLPDDMVEADALDTLVATLNDIGIA 288

Query: 879  VSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            V E   D ETL+L+    N+T++++ EE  EAALSTVDS+FGRT DP++MYMREMG+VEL
Sbjct: 289  VYEQAPDAETLLLNDNAPNVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVEL 348

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN- 993
            LTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  AD+++ +EIKIDE VDGLID N 
Sbjct: 349  LTREGEIEIAKRIEAGLKDMVMAISACPVTIAEILAIADRVANDEIKIDEFVDGLIDPNA 408

Query: 994  -------FSSNNRVIKGNKNNNEEKILIESSSADLST-------EQLEKLKYESLIKFSN 1039
                   FS        ++  +E+                     QLE+LK  SL KF  
Sbjct: 409  EEAGDIDFSGAATAAADDEEQDEDSDEESDEDESDEAAAAGASARQLEELKQASLEKFRI 468

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ +RFTA+++E+LCDTLR Q+++V ++
Sbjct: 469  IADQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTVRFTARNVERLCDTLRGQVDEVRKL 528

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ IL IVV+KCG PR  F+  FP NE NL+W+         Y+ I+ RN+P+++ELQQK
Sbjct: 529  ERAILNIVVDKCGFPRSDFVARFPGNETNLDWIQTLVADNKPYSEIIERNVPAVQELQQK 588

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            LI+LQ  +VLPL +L+ +NRKM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLD
Sbjct: 589  LIDLQARVVLPLPELKQVNRKMSEGEKRAREAKREMTEANLRLVISIAKKYTNRGLQFLD 648

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 649  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 708

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 709  NRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 768

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED N LAP++AAL  SMR V+KD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVT
Sbjct: 769  EDTNTLAPAEAALRDSMRHVMKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVT 828

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR  KLK FLE
Sbjct: 829  RERIRQIEAKALRKLRHPSRSDKLKSFLE 857



 Score =  808 bits (2086), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 405/653 (62%), Positives = 505/653 (77%), Gaps = 21/653 (3%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K + K++K KE  L   F+   +  + EE+E  R+K K +IKLGK RGYLT++EIND LP
Sbjct: 208 KQRAKDRKAKEKALLKEFA-STQPGTEEELELRRQKLKAVIKLGKSRGYLTYAEINDHLP 266

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVD 122
           +D+++ + +++++ T   + I+V E   D ETL+L+    N+T++++ EE  EAALSTVD
Sbjct: 267 DDMVEADALDTLVATLNDIGIAVYEQAPDAETLLLNDNAPNVTTEEEAEEEAEAALSTVD 326

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL  A
Sbjct: 327 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTIAEILAIA 386

Query: 183 DKISKNEIKIDEIVDGLIDKN--------FSSNNRVIKGNKNNNEEKILIESSSADLST- 233
           D+++ +EIKIDE VDGLID N        FS        ++  +E+              
Sbjct: 387 DRVANDEIKIDEFVDGLIDPNAEEAGDIDFSGAATAAADDEEQDEDSDEESDEDESDEAA 446

Query: 234 ------EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
                  QLE+LK  SL KF  I+  FDKMR+AFEKEGY S+ Y+KA   I  E++ +RF
Sbjct: 447 AAGASARQLEELKQASLEKFRIIADQFDKMRRAFEKEGYKSKPYVKAQEAIQAELMTVRF 506

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA+++E+LCDTLR Q+++V ++E+ IL IVV+KCG PR  F+  FP NE NL+W+     
Sbjct: 507 TARNVERLCDTLRGQVDEVRKLERAILNIVVDKCGFPRSDFVARFPGNETNLDWIQTLVA 566

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
               Y+ I+ RN+P+++ELQQKLI+LQ  +VLPL +L+ +NRKM  GE +AR+AKREMTE
Sbjct: 567 DNKPYSEIIERNVPAVQELQQKLIDLQARVVLPLPELKQVNRKMSEGEKRAREAKREMTE 626

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR
Sbjct: 627 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 686

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           SIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIA
Sbjct: 687 SIADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIA 746

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           KEP+SME+P+GDD+DSHLGDFIED N LAP++AAL  SMR V+KD+L+SLTPRE+KVLRM
Sbjct: 747 KEPISMETPIGDDDDSHLGDFIEDTNTLAPAEAALRDSMRHVMKDVLDSLTPREAKVLRM 806

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWLEQRTHQN 639
           RFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L+    +N
Sbjct: 807 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEEN 859


>gi|389872353|ref|YP_006379772.1| RNA polymerase sigma factor RpoD [Advenella kashmirensis WT001]
 gi|388537602|gb|AFK62790.1| RNA polymerase sigma factor RpoD [Advenella kashmirensis WT001]
          Length = 814

 Score =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 397/611 (64%), Positives = 480/611 (78%), Gaps = 9/611 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S EE E  R + K+LIKLGKERGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 207  SPEEQEARRNRLKLLIKLGKERGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 266

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D E L+LS+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMG+VELLTR
Sbjct: 267  QAPDAEALLLSDNAPVASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTR 326

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIEEGLK M+ AI++CPTTI EIL    ++   + +IDEIVDGL+ ++    
Sbjct: 327  EGEIEIAKRIEEGLKHMVMAIAACPTTIQEILNHIQRVRDGQAQIDEIVDGLVTEDGEEY 386

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                       EE    +  +  +S++QLE L+ ++L KF ++   F KMR  +E+ GY 
Sbjct: 387  -----AGSGVQEEDESDDGPAGGMSSKQLEMLRQQALEKFDSVEKWFGKMRTVYEQGGYR 441

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            +  YI+A   I  E++G+RFTAK +E+L DTLRNQ+ +V Q+E+ IL   V++ GMPR +
Sbjct: 442  TPDYIRAQEAILEELMGVRFTAKMVERLADTLRNQVEEVRQLERAILHTCVDRVGMPRSY 501

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FIKVFP  E NLNWV +E      Y   L R+IP I E+QQKLI+L+  +VLPL DL+D+
Sbjct: 502  FIKVFPGQETNLNWVQDEVNKNAAYAETLERSIPDIHEIQQKLIDLENTVVLPLKDLKDV 561

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M+ GE KA+KAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 562  NKRMVTGEAKAKKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 621

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG+EPDP+
Sbjct: 622  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGTEPDPA 681

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPEEKIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSD AL  SMR
Sbjct: 682  TLAQKMDMPEEKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDNATLAPSDNALYGSMR 741

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               K++L+SLTPRE+KVLRMRFGI +SSD TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 742  DAFKEVLDSLTPREAKVLRMRFGIGISSDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 801

Query: 1418 SRYYKLKIFLE 1428
            SR  KLK FLE
Sbjct: 802  SRADKLKSFLE 812



 Score =  800 bits (2065), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/598 (64%), Positives = 470/598 (78%), Gaps = 9/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S EE E  R + K+LIKLGKERGYLT+ EIND LP+D++D E I+ II TF  M ISV +
Sbjct: 207 SPEEQEARRNRLKLLIKLGKERGYLTYGEINDHLPDDLVDAEAIDGIISTFSDMGISVYD 266

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D E L+LS+     +SDDDVE+  EAAL+TVDSDFGRT DP++MYMREMG+VELLTR
Sbjct: 267 QAPDAEALLLSDNAPVASSDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTR 326

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIEEGLK M+ AI++CPTTI EIL    ++   + +IDEIVDGL+ ++    
Sbjct: 327 EGEIEIAKRIEEGLKHMVMAIAACPTTIQEILNHIQRVRDGQAQIDEIVDGLVTEDGEEY 386

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                      EE    +  +  +S++QLE L+ ++L KF ++   F KMR  +E+ GY 
Sbjct: 387 -----AGSGVQEEDESDDGPAGGMSSKQLEMLRQQALEKFDSVEKWFGKMRTVYEQGGYR 441

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           +  YI+A   I  E++G+RFTAK +E+L DTLRNQ+ +V Q+E+ IL   V++ GMPR +
Sbjct: 442 TPDYIRAQEAILEELMGVRFTAKMVERLADTLRNQVEEVRQLERAILHTCVDRVGMPRSY 501

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIKVFP  E NLNWV +E      Y   L R+IP I E+QQKLI+L+  +VLPL DL+D+
Sbjct: 502 FIKVFPGQETNLNWVQDEVNKNAAYAETLERSIPDIHEIQQKLIDLENTVVLPLKDLKDV 561

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M+ GE KA+KAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 562 NKRMVTGEAKAKKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 621

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI+RQILQETG+EPDP+
Sbjct: 622 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRINRQILQETGTEPDPA 681

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPEEKIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED   LAPSD AL  SMR
Sbjct: 682 TLAQKMDMPEEKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDNATLAPSDNALYGSMR 741

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              K++L+SLTPRE+KVLRMRFGI +SSD TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 742 DAFKEVLDSLTPREAKVLRMRFGIGISSDQTLEEVGKQFDVTRERIRQIEAKALRKLR 799


>gi|193884351|dbj|BAG54997.1| Sigma70 [Ralstonia solanacearum]
          Length = 758

 Score =  807 bits (2084), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 401/635 (63%), Positives = 501/635 (78%), Gaps = 17/635 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 105 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 164

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 165 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 224

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 225 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 284

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD------------ 230
           ++++ +E KIDE +DGLID N  +      G+++ + E    + S  +            
Sbjct: 285 ERVANDEAKIDEYIDGLIDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSS 344

Query: 231 -LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTA 289
             S  QLE+LK  +L KF+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA
Sbjct: 345 AASARQLEELKQAALAKFAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTA 404

Query: 290 KSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ 349
           +++E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++      
Sbjct: 405 RNVERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADG 464

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             Y+ I+ RNIP++ ELQQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEAN
Sbjct: 465 KPYSAIVERNIPAVHELQQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEAN 524

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 525 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 584

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKI KIAKE
Sbjct: 585 ADQARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIRKIAKE 644

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+SME+P+GDD+DSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRF
Sbjct: 645 PISMETPIGDDDDSHLGDFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRF 704

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           GIEMS+DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 705 GIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 739



 Score =  798 bits (2062), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/618 (63%), Positives = 492/618 (79%), Gaps = 17/618 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 122  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 181

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 182  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 241

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 242  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 301

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSAD-------------LSTEQLEKLKYESLIK 1036
            ID N  +      G+++ + E    + S  +              S  QLE+LK  +L K
Sbjct: 302  IDPNADAAEAAQAGDEDEDFEDEDADESGDEEEDEDDDGSGSSAASARQLEELKQAALAK 361

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   F+KMR+AFEKEGY S+ Y+KA   I NE++ IRFTA+++E+LCDTLR Q+++V
Sbjct: 362  FAIIGDQFEKMRRAFEKEGYKSKPYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEV 421

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ EL
Sbjct: 422  RKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHEL 481

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            QQKLI+LQ  +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQ
Sbjct: 482  QQKLIDLQARVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQ 541

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 542  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 601

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKI KIAKEP+SME+P+GDD+DSHLG
Sbjct: 602  NKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIRKIAKEPISMETPIGDDDDSHLG 661

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQF
Sbjct: 662  DFIEDTNTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQF 721

Query: 1397 DVTRERIRQIEAKALRKL 1414
            DVTRERIRQIEAKALRKL
Sbjct: 722  DVTRERIRQIEAKALRKL 739


>gi|427403584|ref|ZP_18894466.1| RNA polymerase sigma factor RpoD [Massilia timonae CCUG 45783]
 gi|425717567|gb|EKU80523.1| RNA polymerase sigma factor RpoD [Massilia timonae CCUG 45783]
          Length = 909

 Score =  801 bits (2070), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/627 (62%), Positives = 481/627 (76%), Gaps = 21/627 (3%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S  E+E  R++ K LI +GKERGYLT +EIND LPE+IID E IE II TF  M I+V E
Sbjct: 280  SEAELEKRRQQLKNLINMGKERGYLTHAEINDHLPENIIDPEAIEGIIATFNDMGIAVYE 339

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               + E ++LS+     TS+D+VE A   ALSTVDSDFGRT DP++MYMREMG+V LLTR
Sbjct: 340  RAPEAEMMLLSDQAVTPTSEDEVEAAAATALSTVDSDFGRTTDPVRMYMREMGAVSLLTR 399

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------ 991
            +GEIEIAKRIE+GLKDM+ AIS+CPTTI EI+  + KI+ +E+KID++VDG +D      
Sbjct: 400  EGEIEIAKRIEQGLKDMVQAISACPTTISEIIALSHKIASDELKIDDVVDGFVDLEDTPA 459

Query: 992  -----------KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNI 1040
                                   ++    E      ++A  S EQL +L+  +L KF+ I
Sbjct: 460  PAASVAHAAAAAEEDEEEEEEVEDEEEEGEGGSAGGAAAGYSAEQLAQLRKGALEKFALI 519

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
               FD M  AF+ EGY S +Y +A   IS E+LGIRFTAK +EKLCDTLR Q+++V  IE
Sbjct: 520  EQQFDLMGHAFKNEGYGSPAYEEAQAVISYELLGIRFTAKVVEKLCDTLRGQMDEVRSIE 579

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + +L+I VN+CGMPR HFIKVFP NE +L W D E    + Y+ +L RN+P+IKELQQ++
Sbjct: 580  RAVLDICVNRCGMPRAHFIKVFPGNETDLQWGDREVDCAYPYSAVLSRNLPAIKELQQRM 639

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            I+LQ  + LPL DLR IN++M AGE +AR+AKREMT ANLRLVISIAKKY +RGLQFLDL
Sbjct: 640  IDLQARVALPLADLRKINKQMAAGEKRARQAKREMTVANLRLVISIAKKYINRGLQFLDL 699

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGL+KAVDKFEYRRGYKFSTYATWWIRQAITRSIAD ARTIR+PVHMIETINK++
Sbjct: 700  IQEGNIGLLKAVDKFEYRRGYKFSTYATWWIRQAITRSIADMARTIRVPVHMIETINKMN 759

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQI+QETGSEPD   +A KMEMPE K+R+IMKIAKEP+SME+P+G+D DS LGDFIE
Sbjct: 760  RISRQIMQETGSEPDLPTLAAKMEMPENKVREIMKIAKEPISMETPMGEDGDSQLGDFIE 819

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D   LAP DAAL+ASMR+V+K++L+SLTPRE+KVLRMR+G+EMS+DHTLEEVGKQFDVTR
Sbjct: 820  DNATLAPLDAALHASMRNVIKEVLDSLTPREAKVLRMRYGVEMSNDHTLEEVGKQFDVTR 879

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            ERIRQIEAKA+ KLR PSR  KLK FL
Sbjct: 880  ERIRQIEAKAMSKLRQPSRSDKLKTFL 906



 Score =  789 bits (2037), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 396/656 (60%), Positives = 488/656 (74%), Gaps = 27/656 (4%)

Query: 4   INKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
           +   +K + +K K   + N   F     S  E+E  R++ K LI +GKERGYLT +EIND
Sbjct: 257 LKAASKARERKAKGLGMLNEAGF-----SEAELEKRRQQLKNLINMGKERGYLTHAEIND 311

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LPE+IID E IE II TF  M I+V E   + E ++LS+     TS+D+VE A   ALS
Sbjct: 312 HLPENIIDPEAIEGIIATFNDMGIAVYERAPEAEMMLLSDQAVTPTSEDEVEAAAATALS 371

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDSDFGRT DP++MYMREMG+V LLTR+GEIEIAKRIE+GLKDM+ AIS+CPTTI EI+
Sbjct: 372 TVDSDFGRTTDPVRMYMREMGAVSLLTREGEIEIAKRIEQGLKDMVQAISACPTTISEII 431

Query: 180 IAADKISKNEIKIDEIVDGLID-----------------KNFSSNNRVIKGNKNNNEEKI 222
             + KI+ +E+KID++VDG +D                             ++    E  
Sbjct: 432 ALSHKIASDELKIDDVVDGFVDLEDTPAPAASVAHAAAAAEEDEEEEEEVEDEEEEGEGG 491

Query: 223 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 282
               ++A  S EQL +L+  +L KF+ I   FD M  AF+ EGY S +Y +A   IS E+
Sbjct: 492 SAGGAAAGYSAEQLAQLRKGALEKFALIEQQFDLMGHAFKNEGYGSPAYEEAQAVISYEL 551

Query: 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 342
           LGIRFTAK +EKLCDTLR Q+++V  IE+ +L+I VN+CGMPR HFIKVFP NE +L W 
Sbjct: 552 LGIRFTAKVVEKLCDTLRGQMDEVRSIERAVLDICVNRCGMPRAHFIKVFPGNETDLQWG 611

Query: 343 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           D E    + Y+ +L RN+P+IKELQQ++I+LQ  + LPL DLR IN++M AGE +AR+AK
Sbjct: 612 DREVDCAYPYSAVLSRNLPAIKELQQRMIDLQARVALPLADLRKINKQMAAGEKRARQAK 671

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           REMT ANLRLVISIAKKY +RGLQFLDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWIR
Sbjct: 672 REMTVANLRLVISIAKKYINRGLQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWIR 731

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIAD ARTIR+PVHMIETINK++RISRQI+QETGSEPD   +A KMEMPE K+R+
Sbjct: 732 QAITRSIADMARTIRVPVHMIETINKMNRISRQIMQETGSEPDLPTLAAKMEMPENKVRE 791

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           IMKIAKEP+SME+P+G+D DS LGDFIED   LAP DAAL+ASMR+V+K++L+SLTPRE+
Sbjct: 792 IMKIAKEPISMETPMGEDGDSQLGDFIEDNATLAPLDAALHASMRNVIKEVLDSLTPREA 851

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWLEQRTH 637
           KVLRMR+G+EMS+DHTLEEVGKQFDVTRERIRQIEAKA+ KLR P   D L+   H
Sbjct: 852 KVLRMRYGVEMSNDHTLEEVGKQFDVTRERIRQIEAKAMSKLRQPSRSDKLKTFLH 907


>gi|348618105|ref|ZP_08884637.1| RNA polymerase, sigma 70 (sigma D) factor,rpoD [Candidatus
            Glomeribacter gigasporarum BEG34]
 gi|347816617|emb|CCD29303.1| RNA polymerase, sigma 70 (sigma D) factor,rpoD [Candidatus
            Glomeribacter gigasporarum BEG34]
          Length = 698

 Score =  791 bits (2043), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/628 (62%), Positives = 492/628 (78%), Gaps = 19/628 (3%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+    +N+   +E  R K + LIKLGKER +LT +EIND LPEDI++ E I++II 
Sbjct: 80   KEAFALHAANNA-AGLEERRAKLRALIKLGKERSFLTHAEINDHLPEDIVETEAIDTIIG 138

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M I+V +   D E L+L++     TSDD+VEEA E AL+ VDS+FGRT DP++MYM
Sbjct: 139  TFSDMGIAVVDQAPDAEALLLNDNAPAATSDDEVEEA-EVALTHVDSEFGRTTDPVRMYM 197

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGS+ELL R+ EIEIAKRIE+GLK MI AIS+CPTTI +IL  A  + +++++I+E+V
Sbjct: 198  REMGSIELLNRESEIEIAKRIEDGLKHMIQAISACPTTIAQILELAAHVKQDQLRIEELV 257

Query: 987  DGLID-----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNIS 1041
            DGLID       FS++         + +E    E ++   +  QL +LK  SL +F+ + 
Sbjct: 258  DGLIDLEEDADGFSADF--------SEDENEDDEEAAERANAAQLAELKRVSLDRFTRVG 309

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              FDKMR+A+EKEGY S++Y+KA   I NE+  IRFTA++IE+LCDTLR Q+ +V  IE+
Sbjct: 310  RWFDKMRRAYEKEGYQSKAYLKAQKTIQNELELIRFTARTIERLCDTLRAQVEEVRVIER 369

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
            + L  VV+KC MPR  FI  FP+NE NL+W  +    +  Y++ L R +P I E QQKLI
Sbjct: 370  RTLHTVVDKCRMPRDEFIASFPDNETNLDWAPSLIHARRPYSVALERYLPEIHEHQQKLI 429

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             LQ  IVLPL DL++I+R+M AGE+KAR+AKREM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 430  ELQARIVLPLKDLKEISRQMNAGELKARRAKREMIEANLRLVISIAKKYTNRGLQFLDLI 489

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITR+IADQARTIRIPVHMIETINK++R
Sbjct: 490  QEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKMNR 549

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQILQETG+EPD S +A +MEMPE+KIRKI+KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 550  ISRQILQETGAEPDSSTLAARMEMPEDKIRKILKIAKEPISMETPIGDDEDSHLGDFIED 609

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
             + +AP+DAAL A ++  VK++L +LTPRE+KVLRMRFGIEMS+D+TLEEVGKQFDVTRE
Sbjct: 610  THTVAPADAALQAGLQDAVKELLETLTPREAKVLRMRFGIEMSTDYTLEEVGKQFDVTRE 669

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            RIRQIEAKA+RK RHPSR  KLK FLEG
Sbjct: 670  RIRQIEAKAMRKSRHPSRSDKLKPFLEG 697



 Score =  775 bits (2002), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/631 (61%), Positives = 491/631 (77%), Gaps = 20/631 (3%)

Query: 5   NKKTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
            +K K + ++ +E  LLK AF+    +N+   +E  R K + LIKLGKER +LT +EIND
Sbjct: 63  TEKLKARERRAREKALLKEAFALHAANNA-AGLEERRAKLRALIKLGKERSFLTHAEIND 121

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALS 119
            LPEDI++ E I++II TF  M I+V +   D E L+L++     TSDD+VEEA E AL+
Sbjct: 122 HLPEDIVETEAIDTIIGTFSDMGIAVVDQAPDAEALLLNDNAPAATSDDEVEEA-EVALT 180

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
            VDS+FGRT DP++MYMREMGS+ELL R+ EIEIAKRIE+GLK MI AIS+CPTTI +IL
Sbjct: 181 HVDSEFGRTTDPVRMYMREMGSIELLNRESEIEIAKRIEDGLKHMIQAISACPTTIAQIL 240

Query: 180 IAADKISKNEIKIDEIVDGLID-----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTE 234
             A  + +++++I+E+VDGLID       FS++         + +E    E ++   +  
Sbjct: 241 ELAAHVKQDQLRIEELVDGLIDLEEDADGFSADF--------SEDENEDDEEAAERANAA 292

Query: 235 QLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEK 294
           QL +LK  SL +F+ +   FDKMR+A+EKEGY S++Y+KA   I NE+  IRFTA++IE+
Sbjct: 293 QLAELKRVSLDRFTRVGRWFDKMRRAYEKEGYQSKAYLKAQKTIQNELELIRFTARTIER 352

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNL 354
           LCDTLR Q+ +V  IE++ L  VV+KC MPR  FI  FP+NE NL+W  +    +  Y++
Sbjct: 353 LCDTLRAQVEEVRVIERRTLHTVVDKCRMPRDEFIASFPDNETNLDWAPSLIHARRPYSV 412

Query: 355 ILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVI 414
            L R +P I E QQKLI LQ  IVLPL DL++I+R+M AGE+KAR+AKREM EANLRLVI
Sbjct: 413 ALERYLPEIHEHQQKLIELQARIVLPLKDLKEISRQMNAGELKARRAKREMIEANLRLVI 472

Query: 415 SIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474
           SIAKKYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITR+IADQAR
Sbjct: 473 SIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQAR 532

Query: 475 TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 534
           TIRIPVHMIETINK++RISRQILQETG+EPD S +A +MEMPE+KIRKI+KIAKEP+SME
Sbjct: 533 TIRIPVHMIETINKMNRISRQILQETGAEPDSSTLAARMEMPEDKIRKILKIAKEPISME 592

Query: 535 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMS 594
           +P+GDDEDSHLGDFIED + +AP+DAAL A ++  VK++L +LTPRE+KVLRMRFGIEMS
Sbjct: 593 TPIGDDEDSHLGDFIEDTHTVAPADAALQAGLQDAVKELLETLTPREAKVLRMRFGIEMS 652

Query: 595 SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+TLEEVGKQFDVTRERIRQIEAKA+RK R
Sbjct: 653 TDYTLEEVGKQFDVTRERIRQIEAKAMRKSR 683


>gi|82703177|ref|YP_412743.1| RNA polymerase sigma factor RpoD [Nitrosospira multiformis ATCC
            25196]
 gi|82411242|gb|ABB75351.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosospira multiformis ATCC
            25196]
          Length = 707

 Score =  782 bits (2020), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/627 (62%), Positives = 490/627 (78%), Gaps = 12/627 (1%)

Query: 811  KNAFSFDI-KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 869
            KN+ + D  K+ + +E+E  R + K LI  GKERGYLT++EIND LP+D++D E IE+II
Sbjct: 81   KNSHAKDPEKAAASQELEARRMRLKNLIVQGKERGYLTYAEINDHLPDDMLDAEQIENII 140

Query: 870  KTFRYMDISVSEHVLDTETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
                 + ISV +   D ETL++S      +D+DV E  EAALSTVDS+FGRT DP++MYM
Sbjct: 141  SMINDVGISVYDEAPDAETLLMSETAPTVADEDVVEEAEAALSTVDSEFGRTTDPVRMYM 200

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELLTR+ EIEIAKRIE+GLK MI AIS+CPTTI  IL  AD++SK+E+++DE+V
Sbjct: 201  REMGSVELLTRESEIEIAKRIEDGLKHMIQAISACPTTIAGILEFADRVSKDEMRVDELV 260

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD-----LSTEQLEKLKYESLIKFSNIS 1041
            DGL+D    S   +I    ++   +  + S + D     ++   L KLK ++L +F+ + 
Sbjct: 261  DGLLD---PSTEEIISEEISDESLEQELNSDAEDEDVTAVANANLLKLKNDALERFAVVQ 317

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              +D+M+K  EK+G  +++Y      IS+E++ IRF+AK +E+LCDT R  ++++   E+
Sbjct: 318  KAYDEMQKVLEKKGSGNKAYKDIQEQISSELMAIRFSAKMVERLCDTQRALVDEMRGYER 377

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
            +I+E+ V+K GM R HFIK FP NE NLNWVD E  +   Y+  L R  P I E QQ L+
Sbjct: 378  KIMELCVSKVGMSRNHFIKTFPGNESNLNWVDEEIALGKPYSAALERYRPEIVEQQQNLL 437

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             LQ  + +PL +L++INR+M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 438  ALQKQVGIPLKELKEINRRMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLI 497

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 498  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNR 557

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQILQETG EP+P+V+A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED
Sbjct: 558  ISRQILQETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIED 617

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
               +AP+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRE
Sbjct: 618  SATMAPADAAVYASLRDVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRE 677

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR  +L+ FL+
Sbjct: 678  RIRQIEAKALRKLRHPSRSERLRSFLD 704



 Score =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/614 (62%), Positives = 480/614 (78%), Gaps = 12/614 (1%)

Query: 21  KNAFSFDI-KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 79
           KN+ + D  K+ + +E+E  R + K LI  GKERGYLT++EIND LP+D++D E IE+II
Sbjct: 81  KNSHAKDPEKAAASQELEARRMRLKNLIVQGKERGYLTYAEINDHLPDDMLDAEQIENII 140

Query: 80  KTFRYMDISVSEHVLDTETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYM 136
                + ISV +   D ETL++S      +D+DV E  EAALSTVDS+FGRT DP++MYM
Sbjct: 141 SMINDVGISVYDEAPDAETLLMSETAPTVADEDVVEEAEAALSTVDSEFGRTTDPVRMYM 200

Query: 137 REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
           REMGSVELLTR+ EIEIAKRIE+GLK MI AIS+CPTTI  IL  AD++SK+E+++DE+V
Sbjct: 201 REMGSVELLTRESEIEIAKRIEDGLKHMIQAISACPTTIAGILEFADRVSKDEMRVDELV 260

Query: 197 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD-----LSTEQLEKLKYESLIKFSNIS 251
           DGL+D    S   +I    ++   +  + S + D     ++   L KLK ++L +F+ + 
Sbjct: 261 DGLLD---PSTEEIISEEISDESLEQELNSDAEDEDVTAVANANLLKLKNDALERFAVVQ 317

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
             +D+M+K  EK+G  +++Y      IS+E++ IRF+AK +E+LCDT R  ++++   E+
Sbjct: 318 KAYDEMQKVLEKKGSGNKAYKDIQEQISSELMAIRFSAKMVERLCDTQRALVDEMRGYER 377

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 371
           +I+E+ V+K GM R HFIK FP NE NLNWVD E  +   Y+  L R  P I E QQ L+
Sbjct: 378 KIMELCVSKVGMSRNHFIKTFPGNESNLNWVDEEIALGKPYSAALERYRPEIVEQQQNLL 437

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            LQ  + +PL +L++INR+M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 438 ALQKQVGIPLKELKEINRRMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLI 497

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 498 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNR 557

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           ISRQILQETG EP+P+V+A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED
Sbjct: 558 ISRQILQETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIED 617

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
              +AP+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRE
Sbjct: 618 SATMAPADAAVYASLRDVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRE 677

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 678 RIRQIEAKALRKLR 691


>gi|171464016|ref|YP_001798129.1| RNA polymerase sigma-70 subunit RpoD [Polynucleobacter necessarius
            subsp. necessarius STIR1]
 gi|171193554|gb|ACB44515.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter necessarius
            subsp. necessarius STIR1]
          Length = 900

 Score =  777 bits (2006), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/625 (61%), Positives = 487/625 (77%), Gaps = 16/625 (2%)

Query: 816  FDIKSNSREEIENLRK-KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 874
            F  +    EE + LR+ + K LIK+G  +GYLT  E+ND + +++ D + +E++I     
Sbjct: 278  FAAQQLGTEEQQELRRARLKTLIKMGMSKGYLTQGEMNDVMSDELSDADALETLISLLND 337

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            + I+V E   D ETL+LS+ T+    EE  EAALSTVDS+FGRT DP++MYMREMG+V+L
Sbjct: 338  IGITVYEQAPDAETLILSDNTAAAASEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVDL 397

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEI IAK+IE GLKDM+ A+++CP TI EIL   DKI+  EI+ID+ VDGL+D N 
Sbjct: 398  LTREGEIVIAKKIEAGLKDMVMALAACPVTIAEILSNVDKIASGEIEIDQFVDGLVDPNA 457

Query: 995  SSNNRVIKGNKNNNE-----------EKILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
                  IK      E            +      +A  + +QLE+LK  SL KF+ +   
Sbjct: 458  ED----IKLGPEEPEVDPDAEEGEEDGEDEGGGGAATANAKQLEELKQISLEKFAIVRAQ 513

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
              KMR+AF+K+GYN  +YIKA + I  E+LG R TAKS+EKLCDT+R+Q++QV ++E+ I
Sbjct: 514  AKKMRRAFDKDGYNCPAYIKAQDAIRAELLGFRLTAKSVEKLCDTMRSQVDQVWKLERGI 573

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            + ++V+K G+ R   +K FP+  +NL W D   K    Y+ +L RN+P+I+ELQQKLI++
Sbjct: 574  VSLLVDKVGVNRGEVLKDFPKMSMNLAWTDKLLKENKPYSALLQRNVPAIQELQQKLIDI 633

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            Q ++V+PL +L+++N++MIAGE +AR+AKREMT ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 634  QKNVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLIQE 693

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 694  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 753

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQILQETG EPD + +A+KME+PE+KIRKIMKIAKEPVSME+P+GDDEDSHLGDFIED N
Sbjct: 754  RQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPVSMETPIGDDEDSHLGDFIEDGN 813

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRERI
Sbjct: 814  TLAPAEAALHNSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERI 873

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRK+RHPSR  KLK FLE
Sbjct: 874  RQIEAKALRKMRHPSRSDKLKTFLE 898



 Score =  760 bits (1963), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/634 (59%), Positives = 486/634 (76%), Gaps = 16/634 (2%)

Query: 3   FINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
            +  + K + +K KE  L   F+   +  + E+ E  R + K LIK+G  +GYLT  E+N
Sbjct: 257 VLTDRQKARERKAKEKALLKEFAAQ-QLGTEEQQELRRARLKTLIKMGMSKGYLTQGEMN 315

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAALSTVD 122
           D + +++ D + +E++I     + I+V E   D ETL+LS+ T+    EE  EAALSTVD
Sbjct: 316 DVMSDELSDADALETLISLLNDIGITVYEQAPDAETLILSDNTAAAASEEEAEAALSTVD 375

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+V+LLTR+GEI IAK+IE GLKDM+ A+++CP TI EIL   
Sbjct: 376 SEFGRTTDPVRMYMREMGTVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIAEILSNV 435

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE-----------EKILIESSSADL 231
           DKI+  EI+ID+ VDGL+D N       IK      E            +      +A  
Sbjct: 436 DKIASGEIEIDQFVDGLVDPNAED----IKLGPEEPEVDPDAEEGEEDGEDEGGGGAATA 491

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           + +QLE+LK  SL KF+ +     KMR+AF+K+GYN  +YIKA + I  E+LG R TAKS
Sbjct: 492 NAKQLEELKQISLEKFAIVRAQAKKMRRAFDKDGYNCPAYIKAQDAIRAELLGFRLTAKS 551

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +EKLCDT+R+Q++QV ++E+ I+ ++V+K G+ R   +K FP+  +NL W D   K    
Sbjct: 552 VEKLCDTMRSQVDQVWKLERGIVSLLVDKVGVNRGEVLKDFPKMSMNLAWTDKLLKENKP 611

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ +L RN+P+I+ELQQKLI++Q ++V+PL +L+++N++MIAGE +AR+AKREMT ANLR
Sbjct: 612 YSALLQRNVPAIQELQQKLIDIQKNVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLR 671

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 672 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 731

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG EPD + +A+KME+PE+KIRKIMKIAKEPV
Sbjct: 732 QARTIRIPVHMIETINKMNRISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPV 791

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDDEDSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFG+
Sbjct: 792 SMETPIGDDEDSHLGDFIEDGNTLAPAEAALHNSMRDVVKDVLDSLTPREAKVLRMRFGV 851

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRK+R
Sbjct: 852 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKMR 885


>gi|383758559|ref|YP_005437544.1| RNA polymerase primary sigma factor RpoD [Rubrivivax gelatinosus
            IL144]
 gi|381379228|dbj|BAL96045.1| RNA polymerase primary sigma factor RpoD [Rubrivivax gelatinosus
            IL144]
          Length = 731

 Score =  774 bits (1999), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/619 (62%), Positives = 486/619 (78%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D  + + EE+   R++ K LIK+GK RG+LT  EIND LPE ++D+EI+E+I+    
Sbjct: 111  FGLDEATLTEEEVAKRRQELKTLIKMGKTRGFLTHQEINDHLPEKLVDNEILEAIVSMLN 170

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M I+V E   D  TL+++       +D++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 171  DMGIAVYEQAPDAATLLINGSNTATATDEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 230

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            GSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  ADKI+  E++I E+VDG 
Sbjct: 231  GSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTIAEILAMADKIAAGEMQISEVVDGF 290

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            +  + + +    +     +E+     +  +   T++LE+LK ++L KF  +  HFD+MRK
Sbjct: 291  VSDDEADDYVAEEDFDEFDEDDDDDGAGGSKALTKKLEELKKQALEKFDLLRSHFDRMRK 350

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A+EK+GY S +Y KA  +IS++++ IRFT K+IEKLC  LR Q++ V + E++I +IVV+
Sbjct: 351  AYEKDGYKSPAYNKAQESISDDLMTIRFTVKTIEKLCQILRAQVDDVRRYEREIRKIVVD 410

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL W + E      Y+ +L RN+P+++ELQQKLI+LQ   V+
Sbjct: 411  KCGMPQEQFIKTFPPNVLNLKWAEKEAAAGKPYSAVLGRNLPAVQELQQKLIDLQGRAVV 470

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL+DL++INR M AGE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 471  PLDDLKEINRHMNAGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 530

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 531  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 590

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD   +A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP D
Sbjct: 591  FGFEPDAPTLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNVAPVD 650

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 651  AAMQAGLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 710

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL+HPSR  KL+ +L+
Sbjct: 711  AIRKLKHPSRSDKLRTYLD 729



 Score =  763 bits (1970), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/624 (61%), Positives = 484/624 (77%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  + KE  L   F  D  + + EE+   R++ K LIK+GK RG+LT  EIND L
Sbjct: 93  KPLRMKVSRAKERALMREFGLDEATLTEEEVAKRRQELKTLIKMGKTRGFLTHQEINDHL 152

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           PE ++D+EI+E+I+     M I+V E   D  TL+++       +D++ EEA EAALSTV
Sbjct: 153 PEKLVDNEILEAIVSMLNDMGIAVYEQAPDAATLLINGSNTATATDEEAEEAAEAALSTV 212

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMGSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  
Sbjct: 213 DSEFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTIAEILAM 272

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           ADKI+  E++I E+VDG +  + + +    +     +E+     +  +   T++LE+LK 
Sbjct: 273 ADKIAAGEMQISEVVDGFVSDDEADDYVAEEDFDEFDEDDDDDGAGGSKALTKKLEELKK 332

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L KF  +  HFD+MRKA+EK+GY S +Y KA  +IS++++ IRFT K+IEKLC  LR 
Sbjct: 333 QALEKFDLLRSHFDRMRKAYEKDGYKSPAYNKAQESISDDLMTIRFTVKTIEKLCQILRA 392

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E++I +IVV+KCGMP+  FIK FP N +NL W + E      Y+ +L RN+P
Sbjct: 393 QVDDVRRYEREIRKIVVDKCGMPQEQFIKTFPPNVLNLKWAEKEAAAGKPYSAVLGRNLP 452

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
           +++ELQQKLI+LQ   V+PL+DL++INR M AGE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 453 AVQELQQKLIDLQGRAVVPLDDLKEINRHMNAGEKASRDAKKEMIEANLRLVISIAKKYT 512

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 513 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 572

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD   +A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 573 MIETINKMNRISRQHLQEFGFEPDAPTLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDD 632

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N +AP DAA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 633 DSHLGDFIEDTNNVAPVDAAMQAGLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 692

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKA+RKL+
Sbjct: 693 VGKQFDVTRERIRQIEAKAIRKLK 716


>gi|451936475|ref|YP_007460329.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            oncopeltii TCC290E]
 gi|451777398|gb|AGF48373.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            oncopeltii TCC290E]
          Length = 723

 Score =  771 bits (1991), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/613 (63%), Positives = 485/613 (79%), Gaps = 8/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V +
Sbjct: 115  SQEEYEERRNVLKSLIKLGKDRGYLIYSEINDSLPDDLVDAESIDSIVSTFGDMGITVYD 174

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D +TL+++      ++DDDV++  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 175  QAPDVDTLLMNENAALASNDDDVKDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 234

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   +I ID+++DGLID      
Sbjct: 235  EGEIEIAKRIEDGLKHMIMAISSCPIIVDDILQNIEKIHNEQIPIDDVIDGLIDPEDGEE 294

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               I    NNN      +  +  +S +QLE+LK +SL+KFSNIS  + +M   ++K GY 
Sbjct: 295  YAGIGVADNNN----FDDPVAGGMSIKQLEELKAKSLLKFSNISEIYKQMGDNYKKNGYR 350

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            SE Y     +I  E+LG+RFTAK +E+L D +R+ ++++ QIE+ IL I V+K GM R +
Sbjct: 351  SEKYFDMLRSIQEELLGVRFTAKIVERLADCIRSYVDKIRQIERSILNICVDKVGMARDY 410

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI  F  +EI+LNW+ NE +  + Y+  L   +P I++LQ+KLI+LQ +I+LP+++ ++I
Sbjct: 411  FIGSFVNSEIDLNWIINEIEFGNSYSESLKNYVPIIQDLQKKLIDLQREILLPISEFKEI 470

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N+KM  GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 471  NKKMTMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 530

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPS
Sbjct: 531  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGFEPDPS 590

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
            VI+ KM++PEEKIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   LAPSD+AL+ SM+
Sbjct: 591  VISQKMDIPEEKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLAPSDSALHGSMK 650

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 651  NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 710

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FL+ K
Sbjct: 711  SRADKLKSFLDNK 723



 Score =  752 bits (1941), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/598 (63%), Positives = 474/598 (79%), Gaps = 8/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V +
Sbjct: 115 SQEEYEERRNVLKSLIKLGKDRGYLIYSEINDSLPDDLVDAESIDSIVSTFGDMGITVYD 174

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D +TL+++      ++DDDV++  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 175 QAPDVDTLLMNENAALASNDDDVKDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 234

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   +I ID+++DGLID      
Sbjct: 235 EGEIEIAKRIEDGLKHMIMAISSCPIIVDDILQNIEKIHNEQIPIDDVIDGLIDPEDGEE 294

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
              I    NNN      +  +  +S +QLE+LK +SL+KFSNIS  + +M   ++K GY 
Sbjct: 295 YAGIGVADNNN----FDDPVAGGMSIKQLEELKAKSLLKFSNISEIYKQMGDNYKKNGYR 350

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           SE Y     +I  E+LG+RFTAK +E+L D +R+ ++++ QIE+ IL I V+K GM R +
Sbjct: 351 SEKYFDMLRSIQEELLGVRFTAKIVERLADCIRSYVDKIRQIERSILNICVDKVGMARDY 410

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI  F  +EI+LNW+ NE +  + Y+  L   +P I++LQ+KLI+LQ +I+LP+++ ++I
Sbjct: 411 FIGSFVNSEIDLNWIINEIEFGNSYSESLKNYVPIIQDLQKKLIDLQREILLPISEFKEI 470

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N+KM  GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 471 NKKMTMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 530

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPS
Sbjct: 531 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGFEPDPS 590

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
           VI+ KM++PEEKIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   LAPSD+AL+ SM+
Sbjct: 591 VISQKMDIPEEKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLAPSDSALHGSMK 650

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 651 NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 708


>gi|451823091|ref|YP_007459365.1| DNA-directed RNA polymerase sigma subunit RpoD [Candidatus
            Kinetoplastibacterium desouzaii TCC079E]
 gi|451775891|gb|AGF46932.1| DNA-directed RNA polymerase sigma subunit RpoD [Candidatus
            Kinetoplastibacterium desouzaii TCC079E]
          Length = 748

 Score =  770 bits (1988), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/611 (63%), Positives = 486/611 (79%), Gaps = 8/611 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S+EE E+ R   K LIKLGKE+GYLTFSEIND LP+D+ D E++++I+ TF  M ISV E
Sbjct: 141  SQEEYESRRNNLKNLIKLGKEKGYLTFSEINDTLPDDLFDDEVVDTIVSTFNDMGISVYE 200

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D +TL++S     I++DDDVE+ TE AL+TVDSDFGRT DP++MYMREMG+VELLTR
Sbjct: 201  QAPDVDTLLMSETAPIISNDDDVEDETEVALTTVDSDFGRTTDPVRMYMREMGTVELLTR 260

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIEEGL  MI +IS+CPTT+ EIL+  D++S  +I+IDE+VDGLID +    
Sbjct: 261  EGEIEIAKRIEEGLSLMIASISACPTTLNEILLDIDRVSSGQIQIDEVVDGLIDPDDGEE 320

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               I       EE+   E ++  +S++QLE LK +SL KFS +S   ++M+ A+   GY 
Sbjct: 321  YAGI----GFIEEEEFDEDTTGVMSSKQLENLKTKSLQKFSEVSKLLEQMKFAYYNHGYC 376

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+ Y++A ++I  E++G+RF AK +EKL D++R+ + ++  IE+ IL+I V K GMPR  
Sbjct: 377  SKDYLEAKDSIQKELMGVRFNAKMVEKLADSIRSHMKEIRIIERNILDICVEKAGMPRED 436

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI  F   E NLNW+  +  I   Y  +L      I+ +Q+KL+ +Q  I+LP+ D ++I
Sbjct: 437  FISFFVGKESNLNWLIEDPVINSKYFKLLEPFSLMIQSVQKKLLEIQEKIILPIKDFKEI 496

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M +GE KARKAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 497  NKQMTSGESKARKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 556

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPS
Sbjct: 557  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGMEPDPS 616

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
            V++ +M++PE+KIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   LAPSD+AL+ SMR
Sbjct: 617  VLSKQMDIPEDKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLAPSDSALHGSMR 676

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             +VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVG+QFDVTRERIRQIEAKALRKLRHP
Sbjct: 677  DIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGRQFDVTRERIRQIEAKALRKLRHP 736

Query: 1418 SRYYKLKIFLE 1428
            SR  KLK FL+
Sbjct: 737  SRADKLKSFLD 747



 Score =  752 bits (1942), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 382/628 (60%), Positives = 486/628 (77%), Gaps = 15/628 (2%)

Query: 2   KFINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEI 61
           K INK+ +      K+ + K   S       +EE E+ R   K LIKLGKE+GYLTFSEI
Sbjct: 118 KTINKRGRKSKNDAKDLISKGPIS-------QEEYESRRNNLKNLIKLGKEKGYLTFSEI 170

Query: 62  NDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAA 117
           ND LP+D+ D E++++I+ TF  M ISV E   D +TL++S     I++DDDVE+ TE A
Sbjct: 171 NDTLPDDLFDDEVVDTIVSTFNDMGISVYEQAPDVDTLLMSETAPIISNDDDVEDETEVA 230

Query: 118 LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 177
           L+TVDSDFGRT DP++MYMREMG+VELLTR+GEIEIAKRIEEGL  MI +IS+CPTT+ E
Sbjct: 231 LTTVDSDFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGLSLMIASISACPTTLNE 290

Query: 178 ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 237
           IL+  D++S  +I+IDE+VDGLID +       I       EE+   E ++  +S++QLE
Sbjct: 291 ILLDIDRVSSGQIQIDEVVDGLIDPDDGEEYAGI----GFIEEEEFDEDTTGVMSSKQLE 346

Query: 238 KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 297
            LK +SL KFS +S   ++M+ A+   GY S+ Y++A ++I  E++G+RF AK +EKL D
Sbjct: 347 NLKTKSLQKFSEVSKLLEQMKFAYYNHGYCSKDYLEAKDSIQKELMGVRFNAKMVEKLAD 406

Query: 298 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILC 357
           ++R+ + ++  IE+ IL+I V K GMPR  FI  F   E NLNW+  +  I   Y  +L 
Sbjct: 407 SIRSHMKEIRIIERNILDICVEKAGMPREDFISFFVGKESNLNWLIEDPVINSKYFKLLE 466

Query: 358 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 417
                I+ +Q+KL+ +Q  I+LP+ D ++IN++M +GE KARKAK+EMTEANLRLVISIA
Sbjct: 467 PFSLMIQSVQKKLLEIQEKIILPIKDFKEINKQMTSGESKARKAKKEMTEANLRLVISIA 526

Query: 418 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 477
           KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR
Sbjct: 527 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 586

Query: 478 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537
           IPVHMIETINK++RISRQILQETG EPDPSV++ +M++PE+KIRKI+KIAKEP+SME+ +
Sbjct: 587 IPVHMIETINKMNRISRQILQETGMEPDPSVLSKQMDIPEDKIRKILKIAKEPISMETQI 646

Query: 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 597
           GDD+DSHLGDFIED   LAPSD+AL+ SMR +VK++L+SLTPRE+KVLRMRFGIEM++D 
Sbjct: 647 GDDDDSHLGDFIEDTTTLAPSDSALHGSMRDIVKEVLDSLTPREAKVLRMRFGIEMNTDQ 706

Query: 598 TLEEVGKQFDVTRERIRQIEAKALRKLR 625
           TLEEVG+QFDVTRERIRQIEAKALRKLR
Sbjct: 707 TLEEVGRQFDVTRERIRQIEAKALRKLR 734


>gi|429462740|ref|YP_007184203.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            crithidii (ex Angomonas deanei ATCC 30255)]
 gi|451811509|ref|YP_007447964.1| RNA polymerase primary sigma 70 factor [Candidatus
            Kinetoplastibacterium crithidii TCC036E]
 gi|429338254|gb|AFZ82677.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            crithidii (ex Angomonas deanei ATCC 30255)]
 gi|451776667|gb|AGF47666.1| RNA polymerase primary sigma 70 factor [Candidatus
            Kinetoplastibacterium crithidii TCC036E]
          Length = 745

 Score =  770 bits (1988), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/610 (63%), Positives = 488/610 (80%), Gaps = 8/610 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S+EE EN R   K LIKLGKE+GYLTF EIND LP+D+ D E+ ++++ TF  M I+V +
Sbjct: 139  SQEEYENRRNNLKNLIKLGKEKGYLTFGEINDSLPDDLADDEVFDTVVATFSDMGIAVYD 198

Query: 882  HVLDTETLMLS---NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
               D +TL++S    + S+DDVE+  EAAL+TVDSDFGRT DP++MYMREMG+VELLTR+
Sbjct: 199  KTPDIDTLLMSENNTVISNDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTRE 258

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 998
            GEIEIAKRIE+GL  MI AIS+CPTT+ EIL+  +K++ ++++IDEIVD LID +    N
Sbjct: 259  GEIEIAKRIEDGLSLMISAISACPTTVNEILLDIEKVNNDQLQIDEIVDALIDNSDCDPN 318

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
              I  + + NEE  L++ SS  +S +QLE+L+ +SL KFS ++ HF KM+KA+ + GYNS
Sbjct: 319  --ISFHLSENEE--LLDMSSGIMSAKQLEELRTKSLEKFSAVTSHFKKMQKAYVENGYNS 374

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            E Y++A N I  E++G+RF AK I KL D++R+ + ++  +EK I+ I V+K GMPR  F
Sbjct: 375  EDYLEAKNLIQQELMGVRFNAKMIAKLADSIRSHMQEIRSVEKSIINICVDKVGMPRELF 434

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            ++ F  NE N  W+  E  I   Y   L   +  I+  Q+KL+ +Q  IVLP+ + ++IN
Sbjct: 435  LQCFIGNESNTQWMFAEPIINSKYFQALEPLVLLIQNKQKKLLEIQERIVLPIQEFKEIN 494

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            ++M  GE K+ KAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 495  KQMTTGENKSLKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 554

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPSV
Sbjct: 555  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPSV 614

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            ++ KM++PE+KIRKI+KIAKEP+SME+ +GDD DSHLGDFIED N LAPSD+AL++SM++
Sbjct: 615  LSKKMDIPEDKIRKILKIAKEPISMETQIGDD-DSHLGDFIEDTNTLAPSDSALHSSMKN 673

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
            +VK++L+SLTPRE+KVLRMRFGIEM +D TLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 674  IVKEVLDSLTPREAKVLRMRFGIEMHTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 733

Query: 1419 RYYKLKIFLE 1428
            R  KLK FL+
Sbjct: 734  RAEKLKSFLD 743



 Score =  752 bits (1941), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/597 (63%), Positives = 478/597 (80%), Gaps = 8/597 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S+EE EN R   K LIKLGKE+GYLTF EIND LP+D+ D E+ ++++ TF  M I+V +
Sbjct: 139 SQEEYENRRNNLKNLIKLGKEKGYLTFGEINDSLPDDLADDEVFDTVVATFSDMGIAVYD 198

Query: 92  HVLDTETLMLS---NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
              D +TL++S    + S+DDVE+  EAAL+TVDSDFGRT DP++MYMREMG+VELLTR+
Sbjct: 199 KTPDIDTLLMSENNTVISNDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGTVELLTRE 258

Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 208
           GEIEIAKRIE+GL  MI AIS+CPTT+ EIL+  +K++ ++++IDEIVD LID +    N
Sbjct: 259 GEIEIAKRIEDGLSLMISAISACPTTVNEILLDIEKVNNDQLQIDEIVDALIDNSDCDPN 318

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
             I  + + NEE  L++ SS  +S +QLE+L+ +SL KFS ++ HF KM+KA+ + GYNS
Sbjct: 319 --ISFHLSENEE--LLDMSSGIMSAKQLEELRTKSLEKFSAVTSHFKKMQKAYVENGYNS 374

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           E Y++A N I  E++G+RF AK I KL D++R+ + ++  +EK I+ I V+K GMPR  F
Sbjct: 375 EDYLEAKNLIQQELMGVRFNAKMIAKLADSIRSHMQEIRSVEKSIINICVDKVGMPRELF 434

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           ++ F  NE N  W+  E  I   Y   L   +  I+  Q+KL+ +Q  IVLP+ + ++IN
Sbjct: 435 LQCFIGNESNTQWMFAEPIINSKYFQALEPLVLLIQNKQKKLLEIQERIVLPIQEFKEIN 494

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           ++M  GE K+ KAK+EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 495 KQMTTGENKSLKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 554

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPSV
Sbjct: 555 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPSV 614

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           ++ KM++PE+KIRKI+KIAKEP+SME+ +GDD DSHLGDFIED N LAPSD+AL++SM++
Sbjct: 615 LSKKMDIPEDKIRKILKIAKEPISMETQIGDD-DSHLGDFIEDTNTLAPSDSALHSSMKN 673

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +VK++L+SLTPRE+KVLRMRFGIEM +D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 674 IVKEVLDSLTPREAKVLRMRFGIEMHTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 730


>gi|332527902|ref|ZP_08403939.1| putative RNA polymerase sigma(sigma-70) factor transcription
            regulator protein [Rubrivivax benzoatilyticus JA2]
 gi|332112479|gb|EGJ12272.1| putative RNA polymerase sigma(sigma-70) factor transcription
            regulator protein [Rubrivivax benzoatilyticus JA2]
          Length = 734

 Score =  769 bits (1985), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/619 (62%), Positives = 482/619 (77%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K LIK+GK RG+LT  EIND LPE ++D+EI+E+I+    
Sbjct: 114  FGLDETMLTEEEVAKRRQELKTLIKMGKTRGFLTHQEINDHLPEKLVDNEILEAIVSMLN 173

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M I+V E   D  TL+++       +D++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 174  DMGIAVYEQAPDAATLLINGSNTATATDEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 233

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            GSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  ADKI+  E++I E+VDG 
Sbjct: 234  GSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTIAEILAMADKIAAGEMQISEVVDGF 293

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            +  + + +    +     +E+     +  +   T++LE+LK ++L KF  +  HFD+MRK
Sbjct: 294  VSDDEADDYVAEEDFDEFDEDDDDDGAGGSKALTKKLEELKKQALEKFDLLRSHFDRMRK 353

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A+EK+GY S +Y KA   IS +++ IRFT K+IEKLC  LR Q++ V + E++I +IVV+
Sbjct: 354  AYEKDGYKSPAYNKAQEAISQDLMTIRFTVKTIEKLCQILRAQVDDVRRYEREIRKIVVD 413

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL W + E      Y+ +L RN+P+++ELQQKLI+LQ   V+
Sbjct: 414  KCGMPQEQFIKTFPPNVLNLKWAEKEAAAGKPYSAVLGRNLPAVQELQQKLIDLQGRAVV 473

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL+DL++INR M AGE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 474  PLDDLKEINRHMNAGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 533

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 534  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 593

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD   +A KME+PE+KIRKIM IAKEP+SME+P+GDD+DSHLGDFIED N +AP D
Sbjct: 594  FGFEPDAPTLAEKMEIPEDKIRKIMMIAKEPISMETPIGDDDDSHLGDFIEDTNNVAPVD 653

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 654  AAMQAGLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 713

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL+HPSR  KL+ +L+
Sbjct: 714  AIRKLKHPSRSDKLRTYLD 732



 Score =  758 bits (1957), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 383/624 (61%), Positives = 480/624 (76%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  + KE  L   F  D    + EE+   R++ K LIK+GK RG+LT  EIND L
Sbjct: 96  KPLRMKVSRAKERALMREFGLDETMLTEEEVAKRRQELKTLIKMGKTRGFLTHQEINDHL 155

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           PE ++D+EI+E+I+     M I+V E   D  TL+++       +D++ EEA EAALSTV
Sbjct: 156 PEKLVDNEILEAIVSMLNDMGIAVYEQAPDAATLLINGSNTATATDEEAEEAAEAALSTV 215

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMGSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  
Sbjct: 216 DSEFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTIAEILAM 275

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           ADKI+  E++I E+VDG +  + + +    +     +E+     +  +   T++LE+LK 
Sbjct: 276 ADKIAAGEMQISEVVDGFVSDDEADDYVAEEDFDEFDEDDDDDGAGGSKALTKKLEELKK 335

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L KF  +  HFD+MRKA+EK+GY S +Y KA   IS +++ IRFT K+IEKLC  LR 
Sbjct: 336 QALEKFDLLRSHFDRMRKAYEKDGYKSPAYNKAQEAISQDLMTIRFTVKTIEKLCQILRA 395

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E++I +IVV+KCGMP+  FIK FP N +NL W + E      Y+ +L RN+P
Sbjct: 396 QVDDVRRYEREIRKIVVDKCGMPQEQFIKTFPPNVLNLKWAEKEAAAGKPYSAVLGRNLP 455

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
           +++ELQQKLI+LQ   V+PL+DL++INR M AGE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 456 AVQELQQKLIDLQGRAVVPLDDLKEINRHMNAGEKASRDAKKEMIEANLRLVISIAKKYT 515

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 516 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 575

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD   +A KME+PE+KIRKIM IAKEP+SME+P+GDD+
Sbjct: 576 MIETINKMNRISRQHLQEFGFEPDAPTLAEKMEIPEDKIRKIMMIAKEPISMETPIGDDD 635

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N +AP DAA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 636 DSHLGDFIEDTNNVAPVDAAMQAGLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 695

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKA+RKL+
Sbjct: 696 VGKQFDVTRERIRQIEAKAIRKLK 719


>gi|372487885|ref|YP_005027450.1| sigma-70 family RNA polymerase sigma factor [Dechlorosoma suillum PS]
 gi|359354438|gb|AEV25609.1| RNA polymerase sigma factor, sigma-70 family [Dechlorosoma suillum
            PS]
          Length = 656

 Score =  766 bits (1979), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/614 (63%), Positives = 480/614 (78%), Gaps = 11/614 (1%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            ++E  + + K LIKLGKERG+LT++EIND LP+D++D E IESII TF  M I V +   
Sbjct: 40   DVETRKTRLKTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIITTFNDMGIQVFDEAP 99

Query: 885  DTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
              E L++S+    +  D++VEE  EAALSTVDS+FGRT DP++MYMREMG+VELLTR+GE
Sbjct: 100  AAEDLLMSDNAPAVADDEEVEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGE 159

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            IEIAKRIE+GLK MI AIS+CPTTI EIL  A+K+ K E++IDE++DGLID N +     
Sbjct: 160  IEIAKRIEDGLKHMIQAISACPTTIAEILAMAEKVEKEEMRIDEVIDGLIDPNAAEEELA 219

Query: 1001 IKGNKNNNEEKILIESSS------ADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 1054
             +      ++++            A +S   L+ LK ++L +F+ I   + K  KA   +
Sbjct: 220  AEEAVVEGDDEVEDGDDEEEGGEGAAVSASLLQ-LKTDALERFATIKTLYGKAHKALVSK 278

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G   ++Y+K    IS E++ IRFT+K IE+LCD++R+ ++ V + E++I E+ V K GMP
Sbjct: 279  GSQDKTYLKLQQQISAELMNIRFTSKVIERLCDSVRSMVDSVRERERKIQELCVRKVGMP 338

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R HFIK FP NEINL WV+ E  +   Y  IL R  P+I+E Q+KL+ LQ  I +PL DL
Sbjct: 339  RPHFIKSFPGNEINLEWVEKEIAVAKGYGPILTRTAPNIQEEQRKLLALQDHIGIPLKDL 398

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DIN++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 399  KDINKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 458

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EP
Sbjct: 459  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEP 518

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
            DP+ +AIKMEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED    AP DAAL +
Sbjct: 519  DPATLAIKMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDTATTAPVDAALYS 578

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
             +R V K+IL++LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 579  GLREVTKEILDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 638

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR  KL+ FL+
Sbjct: 639  RHPSRSDKLRSFLD 652



 Score =  750 bits (1936), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/601 (63%), Positives = 470/601 (78%), Gaps = 11/601 (1%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           ++E  + + K LIKLGKERG+LT++EIND LP+D++D E IESII TF  M I V +   
Sbjct: 40  DVETRKTRLKTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIITTFNDMGIQVFDEAP 99

Query: 95  DTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
             E L++S+    +  D++VEE  EAALSTVDS+FGRT DP++MYMREMG+VELLTR+GE
Sbjct: 100 AAEDLLMSDNAPAVADDEEVEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGE 159

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           IEIAKRIE+GLK MI AIS+CPTTI EIL  A+K+ K E++IDE++DGLID N +     
Sbjct: 160 IEIAKRIEDGLKHMIQAISACPTTIAEILAMAEKVEKEEMRIDEVIDGLIDPNAAEEELA 219

Query: 211 IKGNKNNNEEKILIESSS------ADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 264
            +      ++++            A +S   L+ LK ++L +F+ I   + K  KA   +
Sbjct: 220 AEEAVVEGDDEVEDGDDEEEGGEGAAVSASLLQ-LKTDALERFATIKTLYGKAHKALVSK 278

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G   ++Y+K    IS E++ IRFT+K IE+LCD++R+ ++ V + E++I E+ V K GMP
Sbjct: 279 GSQDKTYLKLQQQISAELMNIRFTSKVIERLCDSVRSMVDSVRERERKIQELCVRKVGMP 338

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R HFIK FP NEINL WV+ E  +   Y  IL R  P+I+E Q+KL+ LQ  I +PL DL
Sbjct: 339 RPHFIKSFPGNEINLEWVEKEIAVAKGYGPILTRTAPNIQEEQRKLLALQDHIGIPLKDL 398

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DIN++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 399 KDINKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 458

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EP
Sbjct: 459 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEP 518

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
           DP+ +AIKMEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED    AP DAAL +
Sbjct: 519 DPATLAIKMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDTATTAPVDAALYS 578

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
            +R V K+IL++LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 579 GLREVTKEILDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 638

Query: 625 R 625
           R
Sbjct: 639 R 639


>gi|71906166|ref|YP_283753.1| RNA polymerase sigma factor RpoD [Dechloromonas aromatica RCB]
 gi|71845787|gb|AAZ45283.1| RNA polymerase, sigma 70 subunit, RpoD [Dechloromonas aromatica RCB]
          Length = 657

 Score =  766 bits (1978), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/611 (62%), Positives = 471/611 (77%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LIKLGKERGYLT++EIND LP+D++D E IE+II TF  M I V +     
Sbjct: 43   EARKMRLKALIKLGKERGYLTYAEINDHLPDDVVDAESIEAIISTFSEMSIQVFDEAPAA 102

Query: 887  ETLMLSNITS----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            E L++S+  +    D++VE   E ALSTVDS+FGRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 103  EDLLMSDTAAVAADDEEVEAQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEIE 162

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNN 998
            IAKRIEEGLK MI AI++CPTTI +IL  A K+  +E++IDE+VDGLID N      +  
Sbjct: 163  IAKRIEEGLKHMIQAIAACPTTISDILELAAKVESDEMRIDELVDGLIDPNAVEEAPAAE 222

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
                      +     E +    +   L +LK ++L +F NI     KM+K    +G + 
Sbjct: 223  MPEAEEDEEEDGDDDGEGAGGGAAAASLLQLKTDALERFKNIKGIHAKMQKMLPTKGSHD 282

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            + YIK    +S+E++ IRFT++SIE+LCD++R  + QV   E++I +I V++  MPR HF
Sbjct: 283  KVYIKLLQQVSDELMNIRFTSRSIERLCDSVRGMVEQVRGCERKIQQICVDRVKMPRPHF 342

Query: 1119 IKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            I+ FP NEINL+W D E       Y  IL RN P IKE Q+KL+ LQ  I +PL DL+DI
Sbjct: 343  IQSFPGNEINLDWADAEVAAAPKTYVAILTRNAPDIKEEQKKLLALQDRIGIPLKDLKDI 402

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 403  NKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 462

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 463  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 522

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KM+MPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP+DAA+ +S+R
Sbjct: 523  TLAKKMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDSGTLAPADAAMYSSLR 582

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             V K+IL++LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 583  GVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 642

Query: 1418 SRYYKLKIFLE 1428
            +R  KL+ F++
Sbjct: 643  TRSDKLRSFVD 653



 Score =  752 bits (1941), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/606 (62%), Positives = 464/606 (76%), Gaps = 10/606 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LIKLGKERGYLT++EIND LP+D++D E IE+II TF  M I V +     
Sbjct: 43  EARKMRLKALIKLGKERGYLTYAEINDHLPDDVVDAESIEAIISTFSEMSIQVFDEAPAA 102

Query: 97  ETLMLSNITS----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           E L++S+  +    D++VE   E ALSTVDS+FGRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 103 EDLLMSDTAAVAADDEEVEAQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEIE 162

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNN 208
           IAKRIEEGLK MI AI++CPTTI +IL  A K+  +E++IDE+VDGLID N      +  
Sbjct: 163 IAKRIEEGLKHMIQAIAACPTTISDILELAAKVESDEMRIDELVDGLIDPNAVEEAPAAE 222

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
                     +     E +    +   L +LK ++L +F NI     KM+K    +G + 
Sbjct: 223 MPEAEEDEEEDGDDDGEGAGGGAAAASLLQLKTDALERFKNIKGIHAKMQKMLPTKGSHD 282

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           + YIK    +S+E++ IRFT++SIE+LCD++R  + QV   E++I +I V++  MPR HF
Sbjct: 283 KVYIKLLQQVSDELMNIRFTSRSIERLCDSVRGMVEQVRGCERKIQQICVDRVKMPRPHF 342

Query: 329 IKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           I+ FP NEINL+W D E       Y  IL RN P IKE Q+KL+ LQ  I +PL DL+DI
Sbjct: 343 IQSFPGNEINLDWADAEVAAAPKTYVAILTRNAPDIKEEQKKLLALQDRIGIPLKDLKDI 402

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 403 NKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 462

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+
Sbjct: 463 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPA 522

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KM+MPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP+DAA+ +S+R
Sbjct: 523 TLAKKMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDSGTLAPADAAMYSSLR 582

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-P 626
            V K+IL++LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P
Sbjct: 583 GVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 642

Query: 627 LAHDWL 632
              D L
Sbjct: 643 TRSDKL 648


>gi|124267677|ref|YP_001021681.1| RNA polymerase sigma(sigma-70) factor transcription regulator protein
            [Methylibium petroleiphilum PM1]
 gi|124260452|gb|ABM95446.1| putative RNA polymerase sigma(sigma-70) factor transcription
            regulator protein [Methylibium petroleiphilum PM1]
          Length = 746

 Score =  766 bits (1978), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/619 (60%), Positives = 482/619 (77%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D  + + +E+   R++ K LIK+GK RG+LT  EIND LPE +I+ EI+E+I+    
Sbjct: 126  FGLDETALTEDEVAKRRQELKTLIKMGKTRGFLTHQEINDHLPEKLIEAEILEAIVSMLN 185

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M I+V E   D  TL+++      ++D++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 186  DMGIAVYEQAPDAATLLIAGGSTATSTDEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 245

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL+ M+ AIS  PTTI EIL+ ADKI   E++I E VDG 
Sbjct: 246  GTVELLTREGEIEIAKRIEGGLQAMMLAISESPTTIAEILVLADKIRVGEMQISEAVDGF 305

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            +    + +    +     +EE     +  +   T++LE+LK ++L++F  +  HFD+MRK
Sbjct: 306  VSNEEADDYVAEEDFDEFDEEDDDDGNGGSKALTKKLEELKTQALVRFDELRTHFDRMRK 365

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A+EKEGY S +Y +A   +S+E++ +RFT K+IE+LC  LR+Q++ + + E+++ +IVV+
Sbjct: 366  AYEKEGYKSPAYNRAQMGVSSEIMSLRFTVKTIERLCQILRSQVDDIRRYERELRKIVVD 425

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+ HFIK FP N +NL W + E      Y+ ++ RN+P I++LQQKLI+LQ+  V+
Sbjct: 426  KCGMPQDHFIKTFPPNSLNLKWAEKEIAANKSYSAVMARNLPPIQDLQQKLIDLQSRAVV 485

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            P++DL+ IN+KM  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 486  PIDDLKLINKKMNQGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 545

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 546  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 605

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD   +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP +
Sbjct: 606  FGFEPDAPTLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIE 665

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 666  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 725

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL+HPSR  KL+ +L+
Sbjct: 726  AIRKLKHPSRSDKLRTYLD 744



 Score =  755 bits (1950), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/624 (59%), Positives = 480/624 (76%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  + KE  L   F  D  + + +E+   R++ K LIK+GK RG+LT  EIND L
Sbjct: 108 KPLRMKVSRAKERALMREFGLDETALTEDEVAKRRQELKTLIKMGKTRGFLTHQEINDHL 167

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           PE +I+ EI+E+I+     M I+V E   D  TL+++      ++D++ EE  EAALSTV
Sbjct: 168 PEKLIEAEILEAIVSMLNDMGIAVYEQAPDAATLLIAGGSTATSTDEEAEEEAEAALSTV 227

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL+ M+ AIS  PTTI EIL+ 
Sbjct: 228 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLQAMMLAISESPTTIAEILVL 287

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           ADKI   E++I E VDG +    + +    +     +EE     +  +   T++LE+LK 
Sbjct: 288 ADKIRVGEMQISEAVDGFVSNEEADDYVAEEDFDEFDEEDDDDGNGGSKALTKKLEELKT 347

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L++F  +  HFD+MRKA+EKEGY S +Y +A   +S+E++ +RFT K+IE+LC  LR+
Sbjct: 348 QALVRFDELRTHFDRMRKAYEKEGYKSPAYNRAQMGVSSEIMSLRFTVKTIERLCQILRS 407

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ + + E+++ +IVV+KCGMP+ HFIK FP N +NL W + E      Y+ ++ RN+P
Sbjct: 408 QVDDIRRYERELRKIVVDKCGMPQDHFIKTFPPNSLNLKWAEKEIAANKSYSAVMARNLP 467

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I++LQQKLI+LQ+  V+P++DL+ IN+KM  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 468 PIQDLQQKLIDLQSRAVVPIDDLKLINKKMNQGEKASRDAKKEMIEANLRLVISIAKKYT 527

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 528 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 587

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++R+SRQ LQE G EPD   +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 588 MIETINKMNRLSRQHLQEFGFEPDAPTLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDD 647

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 648 DSHLGDFIEDTNNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 707

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKA+RKL+
Sbjct: 708 VGKQFDVTRERIRQIEAKAIRKLK 731


>gi|334131315|ref|ZP_08505080.1| RNA polymerase sigma factor rpoD, Sigma-70 [Methyloversatilis
            universalis FAM5]
 gi|333443664|gb|EGK71626.1| RNA polymerase sigma factor rpoD, Sigma-70 [Methyloversatilis
            universalis FAM5]
          Length = 674

 Score =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/607 (62%), Positives = 471/607 (77%), Gaps = 8/607 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EIND LP+DI+D E IESII TF  M I V +    +E L
Sbjct: 65   RLRLKTLIALGKERGYLTYAEINDHLPDDIVDAEQIESIISTFNDMGIRVFDEAPASEDL 124

Query: 890  MLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++      +    +VEE  E ALSTV+S+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 125  LMGENAPAVVDASEVEEEAEQALSTVESEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 184

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVI 1001
            RIE+GL+ MI AIS+CPTTI EIL  AD+++++E++IDE++DGLID N     ++     
Sbjct: 185  RIEDGLRHMIQAISACPTTISEILDMADRVARDEMRIDELIDGLIDPNAIEEEAAAASAE 244

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                   E +   E       +  L +LK ++L +F +I   + KM+   +K+G   ++Y
Sbjct: 245  AAEDEEEEGEEEDEDGEGGAMSASLIQLKADALERFESIRTLYTKMQSTLDKKGSQDKTY 304

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +K    +S+E++ IRFTA+ IEKLCD++RN +    + E++ILE+ V+K  MPR HFIKV
Sbjct: 305  LKLQKQLSDELMNIRFTARMIEKLCDSVRNMVESARKHERKILELCVDKGNMPRAHFIKV 364

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE N++W+  E          L R  P+I E Q KLI++Q  I LPL +L+DIN++M
Sbjct: 365  FPGNETNIDWLKGEITAAKANGAQLLRAAPAIIEEQGKLIDIQDRIGLPLKELKDINKQM 424

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 425  STGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 484

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +AI
Sbjct: 485  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAI 544

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP+DAAL AS+R + K
Sbjct: 545  RMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDTATLAPTDAALFASLRDITK 604

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 605  EVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 664

Query: 1422 KLKIFLE 1428
            KL+ FL+
Sbjct: 665  KLRSFLD 671



 Score =  748 bits (1932), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/594 (62%), Positives = 461/594 (77%), Gaps = 8/594 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EIND LP+DI+D E IESII TF  M I V +    +E L
Sbjct: 65  RLRLKTLIALGKERGYLTYAEINDHLPDDIVDAEQIESIISTFNDMGIRVFDEAPASEDL 124

Query: 100 MLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++      +    +VEE  E ALSTV+S+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 125 LMGENAPAVVDASEVEEEAEQALSTVESEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 184

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVI 211
           RIE+GL+ MI AIS+CPTTI EIL  AD+++++E++IDE++DGLID N     ++     
Sbjct: 185 RIEDGLRHMIQAISACPTTISEILDMADRVARDEMRIDELIDGLIDPNAIEEEAAAASAE 244

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                  E +   E       +  L +LK ++L +F +I   + KM+   +K+G   ++Y
Sbjct: 245 AAEDEEEEGEEEDEDGEGGAMSASLIQLKADALERFESIRTLYTKMQSTLDKKGSQDKTY 304

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +K    +S+E++ IRFTA+ IEKLCD++RN +    + E++ILE+ V+K  MPR HFIKV
Sbjct: 305 LKLQKQLSDELMNIRFTARMIEKLCDSVRNMVESARKHERKILELCVDKGNMPRAHFIKV 364

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE N++W+  E          L R  P+I E Q KLI++Q  I LPL +L+DIN++M
Sbjct: 365 FPGNETNIDWLKGEITAAKANGAQLLRAAPAIIEEQGKLIDIQDRIGLPLKELKDINKQM 424

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 425 STGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 484

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +AI
Sbjct: 485 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGAEPDPATLAI 544

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP+DAAL AS+R + K
Sbjct: 545 RMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDTATLAPTDAALFASLRDITK 604

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 605 EVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 658


>gi|375106203|ref|ZP_09752464.1| RNA polymerase sigma factor, sigma-70 family [Burkholderiales
            bacterium JOSHI_001]
 gi|374666934|gb|EHR71719.1| RNA polymerase sigma factor, sigma-70 family [Burkholderiales
            bacterium JOSHI_001]
          Length = 762

 Score =  765 bits (1976), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/619 (62%), Positives = 485/619 (78%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D  + + EE+   R + K LIK+GK RG+LT  EIND LPE ++D+EI+E+I+    
Sbjct: 142  FGLDENTLTEEEVAKRRLELKTLIKMGKTRGFLTHQEINDHLPEKLVDNEILEAIVSMLN 201

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M I+V E   D  TL+++       ++++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 202  DMGIAVYEQAPDAATLLIAGGTTTTATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 261

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            GSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  A KI+  +++I E VDG 
Sbjct: 262  GSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTINEILSMAQKIAGGQMQISEAVDGF 321

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            +  + + +    +     +EE        +   T++LE+LK  +L+KF+ ++ HF+KM K
Sbjct: 322  VSDDEADDYVAEEDFDEFDEEDDDDGQGGSKALTKKLEELKSHALVKFAALALHFEKMSK 381

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A+ KEGY S +Y KA + IS+E++ IRFT K+IE+LCD LR+Q++ V + E++I +IVV+
Sbjct: 382  AYAKEGYRSPAYDKAQHAISDELMTIRFTVKTIERLCDILRSQVDDVRRFEREIRKIVVD 441

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +CGMP+ HFIK FP N +NL W + E      Y+ I+ RN+P+I+ELQQKLI+LQ+  V+
Sbjct: 442  RCGMPQEHFIKTFPPNVLNLKWAEKEIAAAKAYSAIMSRNLPAIQELQQKLIDLQSRAVV 501

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL DL++INRKM AGE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 502  PLEDLKEINRKMNAGEKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 561

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 562  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 621

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD   +A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP +
Sbjct: 622  FGFEPDAPTLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIE 681

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 682  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 741

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL+HPSR  KL+ +L+
Sbjct: 742  AIRKLKHPSRSDKLRTYLD 760



 Score =  754 bits (1947), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/621 (61%), Positives = 482/621 (77%), Gaps = 4/621 (0%)

Query: 9   KIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPED 68
           ++K  + KE  L   F  D  + + EE+   R + K LIK+GK RG+LT  EIND LPE 
Sbjct: 127 RMKVSRAKERALMREFGLDENTLTEEEVAKRRLELKTLIKMGKTRGFLTHQEINDHLPEK 186

Query: 69  IIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSD 124
           ++D+EI+E+I+     M I+V E   D  TL+++       ++++ EEA EAALSTVDS+
Sbjct: 187 LVDNEILEAIVSMLNDMGIAVYEQAPDAATLLIAGGTTTTATEEEAEEAAEAALSTVDSE 246

Query: 125 FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADK 184
           FGRT DP++MYMREMGSVELLTR+GEIEIAKRIE GL+ M+ AIS+ PTTI EIL  A K
Sbjct: 247 FGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEGGLQAMMLAISASPTTINEILSMAQK 306

Query: 185 ISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL 244
           I+  +++I E VDG +  + + +    +     +EE        +   T++LE+LK  +L
Sbjct: 307 IAGGQMQISEAVDGFVSDDEADDYVAEEDFDEFDEEDDDDGQGGSKALTKKLEELKSHAL 366

Query: 245 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 304
           +KF+ ++ HF+KM KA+ KEGY S +Y KA + IS+E++ IRFT K+IE+LCD LR+Q++
Sbjct: 367 VKFAALALHFEKMSKAYAKEGYRSPAYDKAQHAISDELMTIRFTVKTIERLCDILRSQVD 426

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
            V + E++I +IVV++CGMP+ HFIK FP N +NL W + E      Y+ I+ RN+P+I+
Sbjct: 427 DVRRFEREIRKIVVDRCGMPQEHFIKTFPPNVLNLKWAEKEIAAAKAYSAIMSRNLPAIQ 486

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           ELQQKLI+LQ+  V+PL DL++INRKM AGE  +R AK+EM EANLRLVISIAKKYT+RG
Sbjct: 487 ELQQKLIDLQSRAVVPLEDLKEINRKMNAGEKASRDAKKEMIEANLRLVISIAKKYTNRG 546

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 547 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 606

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++R+SRQ LQE G EPD   +A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSH
Sbjct: 607 TINKMNRLSRQHLQEFGFEPDAPTLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSH 666

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED N  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGK
Sbjct: 667 LGDFIEDTNNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGK 726

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKA+RKL+
Sbjct: 727 QFDVTRERIRQIEAKAIRKLK 747


>gi|119899516|ref|YP_934729.1| RNA polymerase sigma factor RpoD [Azoarcus sp. BH72]
 gi|119671929|emb|CAL95843.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 662

 Score =  764 bits (1973), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/621 (61%), Positives = 477/621 (76%), Gaps = 27/621 (4%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 44   RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIQVFDEAPAAEDL 103

Query: 890  MLS-NITSDDDVEEATEA---ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++S N+ +  D + A E    ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 104  LMSDNVATSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 163

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+GLK M+ AIS+CPTTI E+L  AD+++++E++IDE+VDGLID N +S+   +    
Sbjct: 164  RIEDGLKHMVQAISACPTTITEMLDTADRVARDEVRIDELVDGLIDPNAASDEAALS--- 220

Query: 1006 NNNEE------------------KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
              +EE                         SA+ ++  L +LK ++L +F+ I  H+++M
Sbjct: 221  EADEEVTAAADEDADGDDEEEADGDGDGGESANAAS--LLQLKTDALARFAVIREHYERM 278

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
              A  K G    +Y+ A   IS+E+L IRFTAK+IE+LCD++R+ + QV   E+QIL++ 
Sbjct: 279  MAALAKSGSQDIAYLAAQQQISDELLNIRFTAKAIERLCDSVRHMVEQVRTHERQILQLC 338

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V++ GMPR HFIKVFP  E +++W+ +E      Y   L R  P++ E+QQKLI+LQ  I
Sbjct: 339  VDRAGMPRQHFIKVFPGQETSIDWLKDEIASGKSYAEGLMRIHPAVLEVQQKLIDLQDRI 398

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 399  GIPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 458

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQIL
Sbjct: 459  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQIL 518

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QETG+EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP
Sbjct: 519  QETGAEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLAP 578

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            ++AA+ + +R    ++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 579  AEAAMYSGLRDATAEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 638

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR  KL+ FL+
Sbjct: 639  AKALRKLRHPSRSEKLRSFLD 659



 Score =  747 bits (1928), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/608 (61%), Positives = 467/608 (76%), Gaps = 27/608 (4%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 44  RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIQVFDEAPAAEDL 103

Query: 100 MLS-NITSDDDVEEATEA---ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++S N+ +  D + A E    ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 104 LMSDNVATSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 163

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+GLK M+ AIS+CPTTI E+L  AD+++++E++IDE+VDGLID N +S+   +    
Sbjct: 164 RIEDGLKHMVQAISACPTTITEMLDTADRVARDEVRIDELVDGLIDPNAASDEAALS--- 220

Query: 216 NNNEE------------------KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
             +EE                         SA+ ++  L +LK ++L +F+ I  H+++M
Sbjct: 221 EADEEVTAAADEDADGDDEEEADGDGDGGESANAAS--LLQLKTDALARFAVIREHYERM 278

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
             A  K G    +Y+ A   IS+E+L IRFTAK+IE+LCD++R+ + QV   E+QIL++ 
Sbjct: 279 MAALAKSGSQDIAYLAAQQQISDELLNIRFTAKAIERLCDSVRHMVEQVRTHERQILQLC 338

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V++ GMPR HFIKVFP  E +++W+ +E      Y   L R  P++ E+QQKLI+LQ  I
Sbjct: 339 VDRAGMPRQHFIKVFPGQETSIDWLKDEIASGKSYAEGLMRIHPAVLEVQQKLIDLQDRI 398

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 399 GIPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 458

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQIL
Sbjct: 459 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQIL 518

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QETG+EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP
Sbjct: 519 QETGAEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLAP 578

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           ++AA+ + +R    ++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 579 AEAAMYSGLRDATAEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 638

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 639 AKALRKLR 646


>gi|149927883|ref|ZP_01916133.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
 gi|149823322|gb|EDM82555.1| RNA polymerase sigma factor RpoD [Limnobacter sp. MED105]
          Length = 878

 Score =  763 bits (1971), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/617 (61%), Positives = 475/617 (76%), Gaps = 11/617 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            EE+E  R + K LIK+GKERGYLTF+EIND LP+D+ D E+IE+++ TF  M I+V E  
Sbjct: 261  EELELRRNQLKTLIKMGKERGYLTFAEINDHLPDDVTDGEVIEAMVSTFHDMGITVYEQA 320

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D E L++++     TS +D EE  EAALS VDS+FGRT DP++MYMREMG+VELLTR+G
Sbjct: 321  PDAEALLMNDNAPVGTSAEDAEEEAEAALSNVDSEFGRTTDPVRMYMREMGTVELLTREG 380

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----- 994
            EIEIAKRIE GLKDM+ AIS+CP  + +++    +I++    +DE+VDG+ID +      
Sbjct: 381  EIEIAKRIEAGLKDMVQAISACPAIVEDVVGLGQRIAEGLSTVDEVVDGIIDDSITEEMV 440

Query: 995  --SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
              ++       + N +EE+     +++ +S  QLE+LK  SL  F+ I   F K++K   
Sbjct: 441  EAAAPEETNDDDDNEDEEEGNDGGTTSGMSARQLEELKKNSLAVFAEIEKQFAKLKKVRA 500

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
              GYN+ +Y KA   I+ + + IRFTAK +E+LC  LR Q++ V +IE++I +I VN+ G
Sbjct: 501  DGGYNTPAYKKAKEAIAEQFMKIRFTAKQVERLCSILREQVDSVRKIEREIYDIAVNRVG 560

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            +PR  F+  F  +E+   WVD  +     +     RN+P+I ELQQKL+ +Q  + LPLN
Sbjct: 561  VPREQFLDKFRGHEVEAAWVDTFSASNAAWAETWARNVPAINELQQKLVAIQDTVSLPLN 620

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            DLR IN++M++GE +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGN+GLMKAV
Sbjct: 621  DLRAINKQMVSGENRARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAV 680

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG 
Sbjct: 681  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGI 740

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EPDP+ +A +MEMPEEKIRKI+KIAKEP+SME+P+GDD+DSHLGDFIED + LAP DAA 
Sbjct: 741  EPDPATLAERMEMPEEKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDNHTLAPQDAAQ 800

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
             +S+R V KD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 801  YSSLRFVTKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALR 860

Query: 1413 KLRHPSRYYKLKIFLEG 1429
            KLRHPSR  KLK FLEG
Sbjct: 861  KLRHPSRSDKLKSFLEG 877



 Score =  744 bits (1920), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/626 (59%), Positives = 473/626 (75%), Gaps = 11/626 (1%)

Query: 11  KNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDII 70
           +  K K+  L N+      + + EE+E  R + K LIK+GKERGYLTF+EIND LP+D+ 
Sbjct: 238 RGSKAKDKALINSAYLSSANATVEELELRRNQLKTLIKMGKERGYLTFAEINDHLPDDVT 297

Query: 71  DHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFG 126
           D E+IE+++ TF  M I+V E   D E L++++     TS +D EE  EAALS VDS+FG
Sbjct: 298 DGEVIEAMVSTFHDMGITVYEQAPDAEALLMNDNAPVGTSAEDAEEEAEAALSNVDSEFG 357

Query: 127 RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKIS 186
           RT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP  + +++    +I+
Sbjct: 358 RTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVQAISACPAIVEDVVGLGQRIA 417

Query: 187 KNEIKIDEIVDGLIDKNF-------SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL 239
           +    +DE+VDG+ID +        ++       + N +EE+     +++ +S  QLE+L
Sbjct: 418 EGLSTVDEVVDGIIDDSITEEMVEAAAPEETNDDDDNEDEEEGNDGGTTSGMSARQLEEL 477

Query: 240 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 299
           K  SL  F+ I   F K++K     GYN+ +Y KA   I+ + + IRFTAK +E+LC  L
Sbjct: 478 KKNSLAVFAEIEKQFAKLKKVRADGGYNTPAYKKAKEAIAEQFMKIRFTAKQVERLCSIL 537

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
           R Q++ V +IE++I +I VN+ G+PR  F+  F  +E+   WVD  +     +     RN
Sbjct: 538 REQVDSVRKIEREIYDIAVNRVGVPREQFLDKFRGHEVEAAWVDTFSASNAAWAETWARN 597

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
           +P+I ELQQKL+ +Q  + LPLNDLR IN++M++GE +AR AKREM EANLRLVISIAKK
Sbjct: 598 VPAINELQQKLVAIQDTVSLPLNDLRAINKQMVSGENRARLAKREMIEANLRLVISIAKK 657

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 658 YTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 717

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK++RISRQILQETG EPDP+ +A +MEMPEEKIRKI+KIAKEP+SME+P+GD
Sbjct: 718 VHMIETINKMNRISRQILQETGIEPDPATLAERMEMPEEKIRKILKIAKEPISMETPIGD 777

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D+DSHLGDFIED + LAP DAA  +S+R V KD+L+SLTPRE+KVLRMRFGIEMS+DHTL
Sbjct: 778 DDDSHLGDFIEDNHTLAPQDAAQYSSLRFVTKDVLDSLTPREAKVLRMRFGIEMSTDHTL 837

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 838 EEVGKQFDVTRERIRQIEAKALRKLR 863


>gi|394988323|ref|ZP_10381161.1| RNA polymerase sigma factor RpoD [Sulfuricella denitrificans skB26]
 gi|393792781|dbj|GAB70800.1| RNA polymerase sigma factor RpoD [Sulfuricella denitrificans skB26]
          Length = 631

 Score =  763 bits (1970), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 382/615 (62%), Positives = 475/615 (77%), Gaps = 11/615 (1%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            +++  R + K LI LGKERGYLT++EIND LP+D++D E IE II     M ISV +   
Sbjct: 14   DVDARRMRLKTLIVLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMIGDMGISVCDEAP 73

Query: 885  DTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
            D ETL++S+     +D+DV E  EAALSTVDSDFGRT DP++MYMREMGSVELLTR+GEI
Sbjct: 74   DAETLLMSDAAPTVTDEDVVEEAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEI 133

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------- 994
            EIAKRIE+GLK M+ AIS+CPTTI EIL   DK+ ++E+++DE+VDGL++ +        
Sbjct: 134  EIAKRIEDGLKHMVQAISACPTTITEILALVDKVERDEMRVDELVDGLMNADGELEEDIA 193

Query: 995  -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 1053
             S+      G       +   E + A ++   L +LK ++L +F+ I   FDKM+++  K
Sbjct: 194  DSAVEAEEAGEAAEELTEEEEEEAGAAVAAANLAQLKADALERFAVIRKAFDKMQQSLAK 253

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
            +G  ++ Y +    +S E+L IRF+AK +E LC++LR+ + +V   E++I+E+ V K GM
Sbjct: 254  KGPKAKGYKEWQEQVSGELLSIRFSAKQVEFLCESLRSLVEEVRSYEREIMELCVTKSGM 313

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            PR HFIK FP NE NL+WV  E   +  Y   L R   SI + QQ+L++LQ  + +P+ D
Sbjct: 314  PRTHFIKTFPGNENNLDWVLTEIATKKPYCEKLTRFQHSIVDQQQRLLDLQERVRIPIKD 373

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            L++INR+M  GE KAR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 374  LKEINRQMSTGEAKARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 433

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E
Sbjct: 434  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQE 493

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            PDPS +A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   LAP+DAAL 
Sbjct: 494  PDPSELAEKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSTTLAPADAALY 553

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
            AS+R   K++L SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 554  ASLREATKEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 613

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR  +L+ FL+
Sbjct: 614  LRHPSRSERLRSFLD 628



 Score =  747 bits (1928), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/602 (62%), Positives = 465/602 (77%), Gaps = 11/602 (1%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           +++  R + K LI LGKERGYLT++EIND LP+D++D E IE II     M ISV +   
Sbjct: 14  DVDARRMRLKTLIVLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMIGDMGISVCDEAP 73

Query: 95  DTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
           D ETL++S+     +D+DV E  EAALSTVDSDFGRT DP++MYMREMGSVELLTR+GEI
Sbjct: 74  DAETLLMSDAAPTVTDEDVVEEAEAALSTVDSDFGRTTDPVRMYMREMGSVELLTREGEI 133

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------- 204
           EIAKRIE+GLK M+ AIS+CPTTI EIL   DK+ ++E+++DE+VDGL++ +        
Sbjct: 134 EIAKRIEDGLKHMVQAISACPTTITEILALVDKVERDEMRVDELVDGLMNADGELEEDIA 193

Query: 205 -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
            S+      G       +   E + A ++   L +LK ++L +F+ I   FDKM+++  K
Sbjct: 194 DSAVEAEEAGEAAEELTEEEEEEAGAAVAAANLAQLKADALERFAVIRKAFDKMQQSLAK 253

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
           +G  ++ Y +    +S E+L IRF+AK +E LC++LR+ + +V   E++I+E+ V K GM
Sbjct: 254 KGPKAKGYKEWQEQVSGELLSIRFSAKQVEFLCESLRSLVEEVRSYEREIMELCVTKSGM 313

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           PR HFIK FP NE NL+WV  E   +  Y   L R   SI + QQ+L++LQ  + +P+ D
Sbjct: 314 PRTHFIKTFPGNENNLDWVLTEIATKKPYCEKLTRFQHSIVDQQQRLLDLQERVRIPIKD 373

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           L++INR+M  GE KAR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 374 LKEINRQMSTGEAKARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 433

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E
Sbjct: 434 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGQE 493

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           PDPS +A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   LAP+DAAL 
Sbjct: 494 PDPSELAEKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSTTLAPADAALY 553

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
           AS+R   K++L SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 554 ASLREATKEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 613

Query: 624 LR 625
           LR
Sbjct: 614 LR 615


>gi|456064017|ref|YP_007502987.1| RNA polymerase, sigma 70 subunit, RpoD [beta proteobacterium CB]
 gi|455441314|gb|AGG34252.1| RNA polymerase, sigma 70 subunit, RpoD [beta proteobacterium CB]
          Length = 701

 Score =  762 bits (1968), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 388/627 (61%), Positives = 487/627 (77%), Gaps = 23/627 (3%)

Query: 821  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVS 880
             S E+ E  R + K LIK+GK +GYLT  E+ND + +++ D + +E++I     ++I+V 
Sbjct: 77   GSEEQQELRRTRLKTLIKMGKSKGYLTHGEMNDVMSDELSDADALETLISLLNDINITVY 136

Query: 881  EHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 936
            E   D ETL+L+      TS+++ EE  EAAL+TVDS+FGRT DP++MYMREMG+V+LLT
Sbjct: 137  EQAPDAETLLLNENASATTSEEEAEEEAEAALATVDSEFGRTTDPVRMYMREMGTVDLLT 196

Query: 937  RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 996
            R+GEI IAK+IE GLKDM+ A+++CP TI EIL   DKI+  E++ID+ VDGL+D N   
Sbjct: 197  REGEIVIAKKIEAGLKDMVMALAACPVTIGEILTNVDKIASGEMEIDQFVDGLVDPNAED 256

Query: 997  NNRVIKGNKNNNEEKILIESS---------------SADLSTEQLEKLKYESLIKFSNIS 1041
                IK      E     E S               +A  + +QLE+LK  SL KF+ + 
Sbjct: 257  ----IKLGPEEPEVDPDAEESDEEGVEDEGGGGGGGAATANAKQLEELKQISLEKFAIVR 312

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
               DKMR+AF+KEGYN  +YIKA   I  E+LG R TAKS+EKLCDT+R+Q++QV ++E+
Sbjct: 313  TQADKMRRAFDKEGYNCPAYIKAQEAIRGELLGFRLTAKSVEKLCDTMRSQVDQVWKLER 372

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
             I+ ++V+K G+ R   +K FP+  +NL W     K    Y  +L RN+P+I+ELQQKLI
Sbjct: 373  GIVSLLVDKVGVNRGEVLKDFPKMSMNLEWTTKLLKENKPYTALLQRNVPAIQELQQKLI 432

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
            ++QT +VLPL +L+++N++MIAGE +AR+AKREMT ANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 433  DIQTRVVLPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLI 492

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 493  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNR 552

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQILQETG EPD + +A+KME+PE+KIRKIMKIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 553  ISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIED 612

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
             N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTRE
Sbjct: 613  GNTLAPAEAALHDSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRE 672

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRK+RHPSR  KLK FLE
Sbjct: 673  RIRQIEAKALRKMRHPSRSDKLKTFLE 699



 Score =  746 bits (1927), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/642 (59%), Positives = 489/642 (76%), Gaps = 24/642 (3%)

Query: 3   FINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
            +  + K + +K KE  L   F+   +  S E+ E  R + K LIK+GK +GYLT  E+N
Sbjct: 50  VLTDRQKARERKAKEKALLKEFAAQ-QLGSEEQQELRRTRLKTLIKMGKSKGYLTHGEMN 108

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAAL 118
           D + +++ D + +E++I     ++I+V E   D ETL+L+      TS+++ EE  EAAL
Sbjct: 109 DVMSDELSDADALETLISLLNDINITVYEQAPDAETLLLNENASATTSEEEAEEEAEAAL 168

Query: 119 STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEI 178
           +TVDS+FGRT DP++MYMREMG+V+LLTR+GEI IAK+IE GLKDM+ A+++CP TI EI
Sbjct: 169 ATVDSEFGRTTDPVRMYMREMGTVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIGEI 228

Query: 179 LIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESS----------- 227
           L   DKI+  E++ID+ VDGL+D N       IK      E     E S           
Sbjct: 229 LTNVDKIASGEMEIDQFVDGLVDPNAED----IKLGPEEPEVDPDAEESDEEGVEDEGGG 284

Query: 228 ----SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
               +A  + +QLE+LK  SL KF+ +    DKMR+AF+KEGYN  +YIKA   I  E+L
Sbjct: 285 GGGGAATANAKQLEELKQISLEKFAIVRTQADKMRRAFDKEGYNCPAYIKAQEAIRGELL 344

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
           G R TAKS+EKLCDT+R+Q++QV ++E+ I+ ++V+K G+ R   +K FP+  +NL W  
Sbjct: 345 GFRLTAKSVEKLCDTMRSQVDQVWKLERGIVSLLVDKVGVNRGEVLKDFPKMSMNLEWTT 404

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
              K    Y  +L RN+P+I+ELQQKLI++QT +VLPL +L+++N++MIAGE +AR+AKR
Sbjct: 405 KLLKENKPYTALLQRNVPAIQELQQKLIDIQTRVVLPLPELKEVNKQMIAGEKRAREAKR 464

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           EMT ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 465 EMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 524

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPD + +A+KME+PE+KIRKI
Sbjct: 525 AITRSIADQARTIRIPVHMIETINKMNRISRQILQETGHEPDAATLALKMEIPEDKIRKI 584

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           MKIAKEP+SME+P+GDDEDSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+K
Sbjct: 585 MKIAKEPISMETPIGDDEDSHLGDFIEDGNTLAPAEAALHDSMRDVVKDVLDSLTPREAK 644

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VLRMRFG+EMS+DHTLEEVGKQFDVTRERIRQIEAKALRK+R
Sbjct: 645 VLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKMR 686


>gi|451812234|ref|YP_007448688.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            galatii TCC219]
 gi|451778136|gb|AGF49084.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            galatii TCC219]
          Length = 737

 Score =  762 bits (1967), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/613 (63%), Positives = 487/613 (79%), Gaps = 8/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V E
Sbjct: 129  SQEEYEERRNILKSLIKLGKDRGYLIYSEINDSLPDDLVDAEAIDSIVSTFGDMGITVYE 188

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D +TL+++     +++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 189  QAPDVDTLLMNENAALVSNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 248

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   ++ ID++VDGLID      
Sbjct: 249  EGEIEIAKRIEDGLKHMIMAISSCPIIVDDILQNIEKIHNEQVSIDDVVDGLIDPEDGEE 308

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               I    NNN      +  +  +S +QLE+LK +SLIKFSNIS  + KM + + ++GY 
Sbjct: 309  YAGIGVADNNN----FDDPVAGGMSIKQLEELKTKSLIKFSNISKIYKKMEEDYNEKGYR 364

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            SE Y     +I  E+LG+RFTAK  E+L D +R+ I+++ QIE+ IL I V+K GM R +
Sbjct: 365  SEEYFIMLKSIQEELLGVRFTAKIAERLADYIRSYIDKIRQIERAILNICVDKAGMSRDY 424

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI  F  NE++LNW+ NE  I ++Y+  L   +P I++LQ+KL+++Q +I+LP+++ ++I
Sbjct: 425  FIGSFVNNEVDLNWIINEININNNYSESLRNYVPMIQDLQKKLVDIQNEILLPISEFKEI 484

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N+KM  GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 485  NKKMTMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 544

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPS
Sbjct: 545  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGFEPDPS 604

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
            VI+ KM++PE+KIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   LAPSD+AL+ SM+
Sbjct: 605  VISQKMDIPEDKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLAPSDSALHGSMK 664

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 665  NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 724

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FL+ K
Sbjct: 725  SRADKLKSFLDNK 737



 Score =  743 bits (1917), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/598 (63%), Positives = 476/598 (79%), Gaps = 8/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V E
Sbjct: 129 SQEEYEERRNILKSLIKLGKDRGYLIYSEINDSLPDDLVDAEAIDSIVSTFGDMGITVYE 188

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D +TL+++     +++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 189 QAPDVDTLLMNENAALVSNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 248

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   ++ ID++VDGLID      
Sbjct: 249 EGEIEIAKRIEDGLKHMIMAISSCPIIVDDILQNIEKIHNEQVSIDDVVDGLIDPEDGEE 308

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
              I    NNN      +  +  +S +QLE+LK +SLIKFSNIS  + KM + + ++GY 
Sbjct: 309 YAGIGVADNNN----FDDPVAGGMSIKQLEELKTKSLIKFSNISKIYKKMEEDYNEKGYR 364

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           SE Y     +I  E+LG+RFTAK  E+L D +R+ I+++ QIE+ IL I V+K GM R +
Sbjct: 365 SEEYFIMLKSIQEELLGVRFTAKIAERLADYIRSYIDKIRQIERAILNICVDKAGMSRDY 424

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI  F  NE++LNW+ NE  I ++Y+  L   +P I++LQ+KL+++Q +I+LP+++ ++I
Sbjct: 425 FIGSFVNNEVDLNWIINEININNNYSESLRNYVPMIQDLQKKLVDIQNEILLPISEFKEI 484

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N+KM  GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 485 NKKMTMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 544

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDPS
Sbjct: 545 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGFEPDPS 604

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
           VI+ KM++PE+KIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   LAPSD+AL+ SM+
Sbjct: 605 VISQKMDIPEDKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLAPSDSALHGSMK 664

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 665 NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 722


>gi|257092101|ref|YP_003165742.1| RNA polymerase sigma factor RpoD [Candidatus Accumulibacter
            phosphatis clade IIA str. UW-1]
 gi|257044625|gb|ACV33813.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Accumulibacter
            phosphatis clade IIA str. UW-1]
          Length = 648

 Score =  759 bits (1961), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/611 (62%), Positives = 471/611 (77%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LIKLGKERG+LT++EIND LP+D++D E IESII TF  M I V +   D 
Sbjct: 34   ETRKMRLKTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIINTFNDMGIQVYDEAPDA 93

Query: 887  ETLMLSNITSDDD-----VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
            ETL++S+           VEE  E ALSTVDS+FGRT DP++MYMREMGSVELLTR+GEI
Sbjct: 94   ETLLMSDAAPAAGADDADVEEQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEI 153

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
            EIAKRIE+GLK MI AIS+CPTTI EIL  AD+I+++E++IDE++DGLID   S +   +
Sbjct: 154  EIAKRIEDGLKHMIQAISACPTTIAEILNCADRIARDEMRIDELIDGLIDPETSGSLEEL 213

Query: 1002 KGNKNNNEEKILIESSSADLSTEQ---LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
                 +  E    E++ A         L +L+ E L +   I   + K      ++G   
Sbjct: 214  AEELESEAEDEDEEAAEAVEGAAAAASLLRLRTEGLERLERIRAGYTKAHALLLRKGSQD 273

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            + Y++    IS EM+G+RFT+K+IE+LCD++R  + +    E++I  I V+   MPR+HF
Sbjct: 274  KGYLQFQQEISEEMMGMRFTSKTIERLCDSVRAMVEEARACERKIQRICVDTVRMPRVHF 333

Query: 1119 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            IKVFP NE+N++WVD E       Y  +L RN P+IKE Q+KL+ LQ  I +PL +L+DI
Sbjct: 334  IKVFPGNELNIDWVDVEIAAAGKTYGAVLLRNAPNIKEEQKKLLALQDRIGIPLRELKDI 393

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 394  NKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 453

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E DP+
Sbjct: 454  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEADPA 513

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KMEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP++AAL +S+R
Sbjct: 514  TLAKKMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDHATLAPTEAALYSSLR 573

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             + KD+L++LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 574  FITKDVLDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 633

Query: 1418 SRYYKLKIFLE 1428
            SR  KL+ FL+
Sbjct: 634  SRSDKLRSFLD 644



 Score =  743 bits (1918), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/598 (62%), Positives = 461/598 (77%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LIKLGKERG+LT++EIND LP+D++D E IESII TF  M I V +   D 
Sbjct: 34  ETRKMRLKTLIKLGKERGFLTYAEINDHLPDDVVDAEQIESIINTFNDMGIQVYDEAPDA 93

Query: 97  ETLMLSNITSDDD-----VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
           ETL++S+           VEE  E ALSTVDS+FGRT DP++MYMREMGSVELLTR+GEI
Sbjct: 94  ETLLMSDAAPAAGADDADVEEQAEQALSTVDSEFGRTTDPVRMYMREMGSVELLTREGEI 153

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
           EIAKRIE+GLK MI AIS+CPTTI EIL  AD+I+++E++IDE++DGLID   S +   +
Sbjct: 154 EIAKRIEDGLKHMIQAISACPTTIAEILNCADRIARDEMRIDELIDGLIDPETSGSLEEL 213

Query: 212 KGNKNNNEEKILIESSSADLSTEQ---LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
                +  E    E++ A         L +L+ E L +   I   + K      ++G   
Sbjct: 214 AEELESEAEDEDEEAAEAVEGAAAAASLLRLRTEGLERLERIRAGYTKAHALLLRKGSQD 273

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           + Y++    IS EM+G+RFT+K+IE+LCD++R  + +    E++I  I V+   MPR+HF
Sbjct: 274 KGYLQFQQEISEEMMGMRFTSKTIERLCDSVRAMVEEARACERKIQRICVDTVRMPRVHF 333

Query: 329 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           IKVFP NE+N++WVD E       Y  +L RN P+IKE Q+KL+ LQ  I +PL +L+DI
Sbjct: 334 IKVFPGNELNIDWVDVEIAAAGKTYGAVLLRNAPNIKEEQKKLLALQDRIGIPLRELKDI 393

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 394 NKQMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 453

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E DP+
Sbjct: 454 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEADPA 513

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KMEMPEEKIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP++AAL +S+R
Sbjct: 514 TLAKKMEMPEEKIRKILKISKEPISMETPIGDDDDSHLGDFIEDHATLAPTEAALYSSLR 573

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            + KD+L++LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 574 FITKDVLDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 631


>gi|145589878|ref|YP_001156475.1| RNA polymerase sigma-70 subunit RpoD [Polynucleobacter necessarius
            subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048284|gb|ABP34911.1| RNA polymerase, sigma 70 subunit, RpoD [Polynucleobacter necessarius
            subsp. asymbioticus QLW-P1DMWA-1]
          Length = 678

 Score =  759 bits (1959), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/628 (60%), Positives = 488/628 (77%), Gaps = 15/628 (2%)

Query: 816  FDIKSNSREEIENLRK-KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 874
            F  +    EE + LR+ + K LIK+G  +GYLT  E+ND + +++ D + +E++I     
Sbjct: 49   FAAQQLGTEEQQELRRARLKTLIKMGMSKGYLTHGEMNDVMSDELSDADALETLISLLND 108

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREMG 930
            + I+V E   D ETL+LS+ T     EE  E      LSTVDS+FGRT DP++MYMREMG
Sbjct: 109  IGITVYEQAPDAETLILSDNTEAAASEEEAEEKAEAALSTVDSEFGRTTDPVRMYMREMG 168

Query: 931  SVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI 990
            +V+LLTR+GEI IAK+IE GLKDM+ A+++CP TI EI+   DKI+  E++ID+ VDGL+
Sbjct: 169  TVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIAEIMSNVDKIASGEMEIDQFVDGLV 228

Query: 991  DKNFSS----------NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNI 1040
            D N             +    +G++   E++      +A  + +QLE+LK  SL KF+ +
Sbjct: 229  DPNAEDIKLGPEEPEVDPDAEEGDEEGGEDEGGGGGGAATANAKQLEELKQISLEKFAIV 288

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
                +KMR+AF+KEGYN  +YIKA   I  E+LG R TAKS+EKLCDT+R+Q++QV ++E
Sbjct: 289  RAQAEKMRRAFDKEGYNCPAYIKAQEAIRAELLGFRLTAKSVEKLCDTMRSQVDQVWKLE 348

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + I+ ++V+K G+ R   +K FP+  +NL W +   K    Y+ +L RN+P+I+ELQQKL
Sbjct: 349  RGIVNLLVDKVGVNRGEVLKDFPKMSMNLTWTEKLLKENKPYSALLQRNVPAIQELQQKL 408

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            I++QT +V+PL +L+++N++MIAGE +AR+AKREMT ANLRLVISIAKKYT+RGLQFLDL
Sbjct: 409  IDIQTRVVIPLPELKEVNKQMIAGEKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDL 468

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 469  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 528

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQETG EPD + +A+KME+PE+KIRKIMKIAKEP+SME+P+GDDEDSHLGDFIE
Sbjct: 529  RISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIE 588

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFG+EMS+DHTLEEVGKQFDVTR
Sbjct: 589  DGNTLAPAEAALHDSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTR 648

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRK+RHPSR  KLK FLE
Sbjct: 649  ERIRQIEAKALRKMRHPSRSDKLKTFLE 676



 Score =  743 bits (1919), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/637 (58%), Positives = 487/637 (76%), Gaps = 15/637 (2%)

Query: 3   FINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
            +  + K + +K KE  L   F+   +  + E+ E  R + K LIK+G  +GYLT  E+N
Sbjct: 28  VLTDRQKARERKAKEKALLKEFAAQ-QLGTEEQQELRRARLKTLIKMGMSKGYLTHGEMN 86

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----L 118
           D + +++ D + +E++I     + I+V E   D ETL+LS+ T     EE  E      L
Sbjct: 87  DVMSDELSDADALETLISLLNDIGITVYEQAPDAETLILSDNTEAAASEEEAEEKAEAAL 146

Query: 119 STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEI 178
           STVDS+FGRT DP++MYMREMG+V+LLTR+GEI IAK+IE GLKDM+ A+++CP TI EI
Sbjct: 147 STVDSEFGRTTDPVRMYMREMGTVDLLTREGEIVIAKKIEAGLKDMVMALAACPVTIAEI 206

Query: 179 LIAADKISKNEIKIDEIVDGLIDKNFSS----------NNRVIKGNKNNNEEKILIESSS 228
           +   DKI+  E++ID+ VDGL+D N             +    +G++   E++      +
Sbjct: 207 MSNVDKIASGEMEIDQFVDGLVDPNAEDIKLGPEEPEVDPDAEEGDEEGGEDEGGGGGGA 266

Query: 229 ADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           A  + +QLE+LK  SL KF+ +    +KMR+AF+KEGYN  +YIKA   I  E+LG R T
Sbjct: 267 ATANAKQLEELKQISLEKFAIVRAQAEKMRRAFDKEGYNCPAYIKAQEAIRAELLGFRLT 326

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           AKS+EKLCDT+R+Q++QV ++E+ I+ ++V+K G+ R   +K FP+  +NL W +   K 
Sbjct: 327 AKSVEKLCDTMRSQVDQVWKLERGIVNLLVDKVGVNRGEVLKDFPKMSMNLTWTEKLLKE 386

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+ +L RN+P+I+ELQQKLI++QT +V+PL +L+++N++MIAGE +AR+AKREMT A
Sbjct: 387 NKPYSALLQRNVPAIQELQQKLIDIQTRVVIPLPELKEVNKQMIAGEKRAREAKREMTVA 446

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 447 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 506

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG EPD + +A+KME+PE+KIRKIMKIAK
Sbjct: 507 IADQARTIRIPVHMIETINKMNRISRQILQETGHEPDAATLALKMEIPEDKIRKIMKIAK 566

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMR
Sbjct: 567 EPISMETPIGDDEDSHLGDFIEDGNTLAPAEAALHDSMRDVVKDVLDSLTPREAKVLRMR 626

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FG+EMS+DHTLEEVGKQFDVTRERIRQIEAKALRK+R
Sbjct: 627 FGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKMR 663


>gi|438000031|ref|YP_007183764.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            blastocrithidii (ex Strigomonas culicis)]
 gi|451812960|ref|YP_007449413.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            blastocrithidii TCC012E]
 gi|429339265|gb|AFZ83687.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            blastocrithidii (ex Strigomonas culicis)]
 gi|451778929|gb|AGF49809.1| RNA polymerase primary sigma factor [Candidatus Kinetoplastibacterium
            blastocrithidii TCC012E]
          Length = 739

 Score =  758 bits (1957), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/613 (61%), Positives = 479/613 (78%), Gaps = 8/613 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V +
Sbjct: 131  SQEEYEERRNILKSLIKLGKDRGYLIYSEINDSLPDDLVDAEAIDSIVSTFGDMGITVYD 190

Query: 882  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
               D +TL+++      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 191  QAPDVDTLLMNENATLASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 250

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   +I ID+++DGLID      
Sbjct: 251  EGEIEIAKRIEDGLKHMIMAISSCPLIVDDILQNIEKIHNEQISIDDVIDGLIDPEDGEE 310

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               I    +NN      +  S  +S +QLE+LK  SLIKF NI+  + +M   +++ G  
Sbjct: 311  YAGIGVTDSNN----FDDPVSGGMSIKQLEELKTRSLIKFGNIADTYKQMGDNYKENGCR 366

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            +E Y     +I  E+LG+RFTAK +E+L D +R+ I+++ QIE+ IL I ++K GM R +
Sbjct: 367  TEEYFNMLKSIQEELLGVRFTAKIVERLADCIRSYIDKIRQIERSILNICIDKVGMSREY 426

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI  F   E++LNW+  E K  + Y+ +L   +P I++ Q+KLI +Q +I+LP+++ ++I
Sbjct: 427  FIDSFVNREVDLNWIIYEIKNNNSYSDLLKNYVPMIQDFQKKLIEIQDEILLPISEFKEI 486

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N+KMI GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 487  NKKMIMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 546

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE+G EPDPS
Sbjct: 547  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQLLQESGFEPDPS 606

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
            VI+ KM++PEEKIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   L PSD+AL+ SM+
Sbjct: 607  VISQKMDIPEEKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLTPSDSALHGSMK 666

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 667  NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLRHP 726

Query: 1418 SRYYKLKIFLEGK 1430
            SR  KLK FL+ K
Sbjct: 727  SRADKLKSFLDNK 739



 Score =  739 bits (1907), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/598 (61%), Positives = 468/598 (78%), Gaps = 8/598 (1%)

Query: 32  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 91
           S+EE E  R   K LIKLGK+RGYL +SEIND LP+D++D E I+SI+ TF  M I+V +
Sbjct: 131 SQEEYEERRNILKSLIKLGKDRGYLIYSEINDSLPDDLVDAEAIDSIVSTFGDMGITVYD 190

Query: 92  HVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
              D +TL+++      ++DDDVE+  EAAL+TVDSDFGRT DP++MYMREMG VELLTR
Sbjct: 191 QAPDVDTLLMNENATLASNDDDVEDEAEAALTTVDSDFGRTTDPVRMYMREMGIVELLTR 250

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEIEIAKRIE+GLK MI AISSCP  + +IL   +KI   +I ID+++DGLID      
Sbjct: 251 EGEIEIAKRIEDGLKHMIMAISSCPLIVDDILQNIEKIHNEQISIDDVIDGLIDPEDGEE 310

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
              I    +NN      +  S  +S +QLE+LK  SLIKF NI+  + +M   +++ G  
Sbjct: 311 YAGIGVTDSNN----FDDPVSGGMSIKQLEELKTRSLIKFGNIADTYKQMGDNYKENGCR 366

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           +E Y     +I  E+LG+RFTAK +E+L D +R+ I+++ QIE+ IL I ++K GM R +
Sbjct: 367 TEEYFNMLKSIQEELLGVRFTAKIVERLADCIRSYIDKIRQIERSILNICIDKVGMSREY 426

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI  F   E++LNW+  E K  + Y+ +L   +P I++ Q+KLI +Q +I+LP+++ ++I
Sbjct: 427 FIDSFVNREVDLNWIIYEIKNNNSYSDLLKNYVPMIQDFQKKLIEIQDEILLPISEFKEI 486

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N+KMI GE  ARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 487 NKKMIMGEAMARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 546

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE+G EPDPS
Sbjct: 547 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQLLQESGFEPDPS 606

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
           VI+ KM++PEEKIRKI+KIAKEP+SME+ +GDD+DSHLGDFIED   L PSD+AL+ SM+
Sbjct: 607 VISQKMDIPEEKIRKILKIAKEPISMETQIGDDDDSHLGDFIEDTTTLTPSDSALHGSMK 666

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++VK++L+SLTPRE+KVLRMRFGIEM++D TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 667 NIVKEVLDSLTPREAKVLRMRFGIEMNTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 724


>gi|299533869|ref|ZP_07047236.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
 gi|298718153|gb|EFI59143.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni S44]
          Length = 815

 Score =  758 bits (1957), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/619 (60%), Positives = 475/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K+LIKLGK RGYLT +EIND LP+ ++D E +E +I    
Sbjct: 195  FGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLN 254

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N       EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 255  DMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 314

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  A++I + ++ I  +VDG 
Sbjct: 315  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVDGF 374

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++ N + +    +     +EE        +   T++LE+LK E+L +F ++   FDKM K
Sbjct: 375  VNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKNEALGRFDSMRELFDKMHK 434

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R Q++ V + E+++ +I+V+
Sbjct: 435  VYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVD 494

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP ++ELQQ LI+LQ  +V+
Sbjct: 495  KCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIPPVQELQQNLIDLQARVVV 554

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 555  PLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 614

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 615  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 674

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 675  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPID 734

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 735  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 794

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 795  ALRKLKHPSRSDKLRSFID 813



 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/624 (59%), Positives = 473/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K+LIKLGK RGYLT +EIND L
Sbjct: 177 KPLRMKISKAKERALMKEFGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHL 236

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 237 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTV 296

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 297 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNM 356

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  +VDG ++ N + +    +     +EE        +   T++LE+LK 
Sbjct: 357 AEEIREGKVVISTVVDGFVNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKN 416

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F ++   FDKM K ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R 
Sbjct: 417 EALGRFDSMRELFDKMHKVYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRA 476

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++ +I+V+KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP
Sbjct: 477 QVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIP 536

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI+LQ  +V+PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 537 PVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYT 596

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 597 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 656

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 657 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 716

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 717 DSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 776

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 777 VGKQFDVTRERIRQIEAKALRKLK 800


>gi|264677331|ref|YP_003277237.1| RNA polymerase sigma-70 subunit RpoD [Comamonas testosteroni CNB-2]
 gi|418530413|ref|ZP_13096336.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni ATCC
            11996]
 gi|262207843|gb|ACY31941.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni CNB-2]
 gi|371452132|gb|EHN65161.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni ATCC
            11996]
          Length = 815

 Score =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/619 (60%), Positives = 475/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K+LIKLGK RGYLT +EIND LP+ ++D E +E +I    
Sbjct: 195  FGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLN 254

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N       EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 255  DMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 314

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  A++I + ++ I  +VDG 
Sbjct: 315  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVDGF 374

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++ N + +    +     +EE        +   T++LE+LK E+L +F ++   FDKM K
Sbjct: 375  VNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKNEALGRFDSMRELFDKMHK 434

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R Q++ V + E+++ +I+V+
Sbjct: 435  VYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVD 494

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP ++ELQQ LI+LQ  +V+
Sbjct: 495  KCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIPPVQELQQNLIDLQARVVV 554

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 555  PLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 614

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 615  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 674

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 675  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPID 734

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 735  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 794

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 795  ALRKLKHPSRSDKLRSFID 813



 Score =  748 bits (1930), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/624 (59%), Positives = 473/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K+LIKLGK RGYLT +EIND L
Sbjct: 177 KPLRMKISKAKERALMKEFGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHL 236

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 237 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTV 296

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 297 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNM 356

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  +VDG ++ N + +    +     +EE        +   T++LE+LK 
Sbjct: 357 AEEIREGKVVISTVVDGFVNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKN 416

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F ++   FDKM K ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R 
Sbjct: 417 EALGRFDSMRELFDKMHKVYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRA 476

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++ +I+V+KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP
Sbjct: 477 QVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIP 536

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI+LQ  +V+PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 537 PVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYT 596

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 597 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 656

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 657 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 716

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 717 DSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 776

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 777 VGKQFDVTRERIRQIEAKALRKLK 800


>gi|221068481|ref|ZP_03544586.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni KF-1]
 gi|220713504|gb|EED68872.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni KF-1]
          Length = 815

 Score =  757 bits (1954), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/619 (60%), Positives = 475/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K+LIKLGK RGYLT +EIND LP+ ++D E +E +I    
Sbjct: 195  FGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHLPDKLVDAETLEVVISMLN 254

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N       EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 255  DMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 314

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  A++I + ++ I  +VDG 
Sbjct: 315  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMAEEIREGKVVISTVVDGF 374

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++ N + +    +     +EE        +   T++LE+LK E+L +F ++   FDKM K
Sbjct: 375  VNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKNEALGRFDSMRELFDKMHK 434

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R Q++ V + E+++ +I+V+
Sbjct: 435  VYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVD 494

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP ++ELQQ LI+LQ  +V+
Sbjct: 495  KCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIPPVQELQQNLIDLQARVVV 554

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 555  PLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 614

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 615  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 674

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 675  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGNNTAPID 734

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 735  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 794

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 795  ALRKLKHPSRSDKLRSFID 813



 Score =  747 bits (1928), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/624 (59%), Positives = 473/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K+LIKLGK RGYLT +EIND L
Sbjct: 177 KPLRMKISKAKERALMKEFGLDETVLTEEEMNTRRQRLKMLIKLGKTRGYLTHAEINDHL 236

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 237 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTV 296

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 297 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNM 356

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  +VDG ++ N + +    +     +EE        +   T++LE+LK 
Sbjct: 357 AEEIREGKVVISTVVDGFVNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKN 416

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F ++   FDKM K ++KEGY +E+Y+K    I+ E++ IRFTAK+IEKLCD +R 
Sbjct: 417 EALGRFDSMRELFDKMHKVYDKEGYGTEAYMKVQKAITEELMTIRFTAKTIEKLCDLVRA 476

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++ +I+V+KCGMP+  FIK FP N +NL+WV  +     +Y+ +L RNIP
Sbjct: 477 QVDDVRKKERELRKIIVDKCGMPQEQFIKDFPPNLLNLDWVIKQVAAGKNYSAVLERNIP 536

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI+LQ  +V+PL +L+ IN++M +GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 537 PVQELQQNLIDLQARVVVPLEELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYT 596

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 597 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 656

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 657 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 716

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 717 DSHLGDFIEDGNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 776

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 777 VGKQFDVTRERIRQIEAKALRKLK 800


>gi|296136130|ref|YP_003643372.1| RNA polymerase sigma-70 subunit RpoD [Thiomonas intermedia K12]
 gi|295796252|gb|ADG31042.1| RNA polymerase, sigma 70 subunit, RpoD [Thiomonas intermedia K12]
          Length = 778

 Score =  751 bits (1939), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/623 (59%), Positives = 490/623 (78%), Gaps = 11/623 (1%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F +D  + + EE+   R + K LIK+GK RG+LT+ EIND +P+++ D E++E+I+    
Sbjct: 157  FGYDDSNITDEELGRRRARLKSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLN 216

Query: 874  YMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D +TL+L+      +S+++ EE  EAALS VDS+FGRT DP++MYMREM
Sbjct: 217  DVGIAVYETTPDAQTLLLNQHGPTASSEEEAEEEAEAALSNVDSEFGRTTDPVRMYMREM 276

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEI IAKRIE+GL+ M+ AIS+ P+T+ EIL  A +I   E+ +DE+VDG+
Sbjct: 277  GTVELLTREGEIVIAKRIEDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVDGM 336

Query: 990  IDKN----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
            +  +    + +   V      + EE    E   A  ++ +LE+LK ++L  F+++   F 
Sbjct: 337  VSDDESDDYVAEEDVDYSLDESGEED---EDGGAGATSMKLEELKGKALEAFADVHDAFM 393

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            KMR+A++K+GY S SY+KA   IS  ++ +RFTA+++EKLC+ LR Q+++V + E++I  
Sbjct: 394  KMRRAYDKDGYRSASYLKAQEAISAALMEVRFTARTVEKLCNLLRAQVDEVRRYEREIRR 453

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V++CGMP+  FIK FP ++++L WVD        Y++IL RN+P+IKELQQ+LI++QT
Sbjct: 454  YAVDRCGMPQEEFIKSFPGHQLDLKWVDKHVASGKPYSVILSRNVPAIKELQQRLIDIQT 513

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             +V+PL+DL++IN +M  GE  AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 514  RVVVPLDDLKEINTQMSLGEQAAREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 573

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            +GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 574  VGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKVNRISRQ 633

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQETG+EPD +V+A KMEMPE+K+RKI+KIA+EP+SME+P+GDD+DSHLGDFIED   L
Sbjct: 634  HLQETGTEPDAAVLAEKMEMPEDKVRKILKIAREPISMETPIGDDDDSHLGDFIEDSGTL 693

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            AP++AA+ A +R VVK+IL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQ
Sbjct: 694  APTEAAMQAGLRDVVKEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQ 753

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKL+HP+R  KL+ FL+
Sbjct: 754  IEAKALRKLKHPTRSDKLRSFLD 776



 Score =  738 bits (1906), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/635 (58%), Positives = 493/635 (77%), Gaps = 13/635 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           KT+  ++  ++ LLK  F +D  + + EE+   R + K LIK+GK RG+LT+ EIND +P
Sbjct: 141 KTRKASRAREKQLLKE-FGYDDSNITDEELGRRRARLKSLIKMGKTRGFLTYGEINDHIP 199

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVD 122
           +++ D E++E+I+     + I+V E   D +TL+L+      +S+++ EE  EAALS VD
Sbjct: 200 DNLADPELMETIVSMLNDVGIAVYETTPDAQTLLLNQHGPTASSEEEAEEEAEAALSNVD 259

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE+GL+ M+ AIS+ P+T+ EIL  A
Sbjct: 260 SEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEDGLRQMMLAISASPSTVAEILAMA 319

Query: 183 DKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEK 238
            +I   E+ +DE+VDG++  +    + +   V      + EE    E   A  ++ +LE+
Sbjct: 320 ARIHHGELPVDEVVDGMVSDDESDDYVAEEDVDYSLDESGEED---EDGGAGATSMKLEE 376

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK ++L  F+++   F KMR+A++K+GY S SY+KA   IS  ++ +RFTA+++EKLC+ 
Sbjct: 377 LKGKALEAFADVHDAFMKMRRAYDKDGYRSASYLKAQEAISAALMEVRFTARTVEKLCNL 436

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR Q+++V + E++I    V++CGMP+  FIK FP ++++L WVD        Y++IL R
Sbjct: 437 LRAQVDEVRRYEREIRRYAVDRCGMPQEEFIKSFPGHQLDLKWVDKHVASGKPYSVILSR 496

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
           N+P+IKELQQ+LI++QT +V+PL+DL++IN +M  GE  AR+AKREM EANLRLVISIAK
Sbjct: 497 NVPAIKELQQRLIDIQTRVVVPLDDLKEINTQMSLGEQAAREAKREMIEANLRLVISIAK 556

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 557 KYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 616

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQ LQETG+EPD +V+A KMEMPE+K+RKI+KIA+EP+SME+P+G
Sbjct: 617 PVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDKVRKILKIAREPISMETPIG 676

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED   LAP++AA+ A +R VVK+IL+SLTPRE+KVLRMRFGIEM++DHT
Sbjct: 677 DDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTPREAKVLRMRFGIEMANDHT 736

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           LEEVGKQFDVTRERIRQIEAKALRKL+ P   D L
Sbjct: 737 LEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKL 771


>gi|410693940|ref|YP_003624562.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
 gi|294340365|emb|CAZ88746.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
          Length = 778

 Score =  751 bits (1938), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/623 (59%), Positives = 490/623 (78%), Gaps = 11/623 (1%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F +D  + + EE+   R + K LIK+GK RG+LT+ EIND +P+++ D E++E+I+    
Sbjct: 157  FGYDDSNITDEELGRRRARLKSLIKMGKTRGFLTYGEINDHIPDNLADPELMETIVSMLN 216

Query: 874  YMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D +TL+L+      +S+++ EE  EAALS VDS+FGRT DP++MYMREM
Sbjct: 217  DVGIAVYETTPDAQTLLLNQHGPTASSEEEAEEEAEAALSNVDSEFGRTTDPVRMYMREM 276

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEI IAKRIE+GL+ M+ AIS+ P+T+ EIL  A +I   E+ +DE+VDG+
Sbjct: 277  GTVELLTREGEIVIAKRIEDGLRQMMLAISASPSTVAEILAMAARIHHGELPVDEVVDGM 336

Query: 990  IDKN----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
            +  +    + +   V      + EE    E   A  ++ +LE+LK ++L  F+++   F 
Sbjct: 337  VSDDESDDYVAEEDVDYSLDESGEED---EDGGAGATSMKLEELKGKALEAFADVHDAFM 393

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            KMR+A++K+GY S SY+KA   IS  ++ +RFTA+++EKLC+ LR Q+++V + E++I  
Sbjct: 394  KMRRAYDKDGYRSASYLKAQEAISAALMEVRFTARTVEKLCNLLRAQVDEVRRYEREIRR 453

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V++CGMP+  FIK FP ++++L WVD        Y++IL RN+P+IKELQQKLI++QT
Sbjct: 454  YAVDRCGMPQEEFIKSFPGHQLDLKWVDKHVASGKPYSVILSRNVPAIKELQQKLIDIQT 513

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             +V+PL+DL++IN +M  GE  AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 514  RVVVPLDDLKEINTQMSLGEQAAREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 573

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            +GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 574  VGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKVNRISRQ 633

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQETG+EPD +V+A KMEMPE+K+RKI+KIA+EP+SME+P+GDD+DSHLGDFIED   L
Sbjct: 634  HLQETGTEPDAAVLAEKMEMPEDKVRKILKIAREPISMETPIGDDDDSHLGDFIEDSGTL 693

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            AP++AA+ A +R VVK+IL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQ
Sbjct: 694  APTEAAMQAGLRDVVKEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQ 753

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKL+HP+R  KL+ FL+
Sbjct: 754  IEAKALRKLKHPTRSDKLRSFLD 776



 Score =  738 bits (1905), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/635 (58%), Positives = 493/635 (77%), Gaps = 13/635 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           KT+  ++  ++ LLK  F +D  + + EE+   R + K LIK+GK RG+LT+ EIND +P
Sbjct: 141 KTRKASRAREKQLLKE-FGYDDSNITDEELGRRRARLKSLIKMGKTRGFLTYGEINDHIP 199

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS----NITSDDDVEEATEAALSTVD 122
           +++ D E++E+I+     + I+V E   D +TL+L+      +S+++ EE  EAALS VD
Sbjct: 200 DNLADPELMETIVSMLNDVGIAVYETTPDAQTLLLNQHGPTASSEEEAEEEAEAALSNVD 259

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEI IAKRIE+GL+ M+ AIS+ P+T+ EIL  A
Sbjct: 260 SEFGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEDGLRQMMLAISASPSTVAEILAMA 319

Query: 183 DKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEK 238
            +I   E+ +DE+VDG++  +    + +   V      + EE    E   A  ++ +LE+
Sbjct: 320 ARIHHGELPVDEVVDGMVSDDESDDYVAEEDVDYSLDESGEED---EDGGAGATSMKLEE 376

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK ++L  F+++   F KMR+A++K+GY S SY+KA   IS  ++ +RFTA+++EKLC+ 
Sbjct: 377 LKGKALEAFADVHDAFMKMRRAYDKDGYRSASYLKAQEAISAALMEVRFTARTVEKLCNL 436

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR Q+++V + E++I    V++CGMP+  FIK FP ++++L WVD        Y++IL R
Sbjct: 437 LRAQVDEVRRYEREIRRYAVDRCGMPQEEFIKSFPGHQLDLKWVDKHVASGKPYSVILSR 496

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
           N+P+IKELQQKLI++QT +V+PL+DL++IN +M  GE  AR+AKREM EANLRLVISIAK
Sbjct: 497 NVPAIKELQQKLIDIQTRVVVPLDDLKEINTQMSLGEQAAREAKREMIEANLRLVISIAK 556

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 557 KYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 616

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQ LQETG+EPD +V+A KMEMPE+K+RKI+KIA+EP+SME+P+G
Sbjct: 617 PVHMIETINKVNRISRQHLQETGTEPDAAVLAEKMEMPEDKVRKILKIAREPISMETPIG 676

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED   LAP++AA+ A +R VVK+IL+SLTPRE+KVLRMRFGIEM++DHT
Sbjct: 677 DDDDSHLGDFIEDSGTLAPTEAAMQAGLRDVVKEILDSLTPREAKVLRMRFGIEMANDHT 736

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           LEEVGKQFDVTRERIRQIEAKALRKL+ P   D L
Sbjct: 737 LEEVGKQFDVTRERIRQIEAKALRKLKHPTRSDKL 771


>gi|171059243|ref|YP_001791592.1| RNA polymerase sigma-70 subunit RpoD [Leptothrix cholodnii SP-6]
 gi|170776688|gb|ACB34827.1| RNA polymerase, sigma 70 subunit, RpoD [Leptothrix cholodnii SP-6]
          Length = 754

 Score =  750 bits (1937), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/619 (59%), Positives = 474/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R + K LIK+GK RG+LT  EIND LPE +++ EI+E+I+    
Sbjct: 134  FGLDETMLTEEEVAKRRSELKTLIKMGKTRGFLTHQEINDHLPEKLVEAEILEAIVSMLN 193

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M I+V E   D  TL+++   +    EE  E A    LSTVDS+FGRT DP++MYMREM
Sbjct: 194  DMGIAVYEQAPDAATLLIAGGGTTTSTEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 253

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI E+L  A+KI      I  +VDG 
Sbjct: 254  GTVELLTREGEIEIAKRIEGGLQAMMLAISASPATIAEVLEMANKIRAGTDPISSVVDGF 313

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            +  + + +    +     +EE+    +  +   T++LE+LK ++L+KF  +   FDKMRK
Sbjct: 314  VAADEADDYVAEEDFDEFDEEEDDDGNGGSKALTKKLEELKNQALVKFDALQLDFDKMRK 373

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A++K+GY S +Y KA   IS +++ +RFT K+IEKLCD LR+Q++ + + E+++ +IVV+
Sbjct: 374  AYDKDGYKSPAYNKAQEAISGQLMTVRFTVKTIEKLCDLLRSQVDDIRRFERELRKIVVD 433

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +CGMP+ +FIK FP N +NL W +NE      Y+ ++ RN+P+I+ELQQKL +LQT  V+
Sbjct: 434  RCGMPQEYFIKSFPPNILNLEWAENEIAANKPYSAVMSRNLPAIQELQQKLTDLQTKAVV 493

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            P++DL+ INR+M  GE  +R+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 494  PIDDLKQINRRMNEGEASSREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 553

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 554  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 613

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD   +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP +
Sbjct: 614  FGFEPDAPSLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPIE 673

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ + +R VV+DIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 674  AAMQSGLRDVVRDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 733

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL+HPSR  KL+ +L+
Sbjct: 734  AIRKLKHPSRSDKLRTYLD 752



 Score =  739 bits (1909), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/624 (58%), Positives = 472/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  + KE  L   F  D    + EE+   R + K LIK+GK RG+LT  EIND L
Sbjct: 116 KPLRMKVSRAKERALMREFGLDETMLTEEEVAKRRSELKTLIKMGKTRGFLTHQEINDHL 175

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           PE +++ EI+E+I+     M I+V E   D  TL+++   +    EE  E A    LSTV
Sbjct: 176 PEKLVEAEILEAIVSMLNDMGIAVYEQAPDAATLLIAGGGTTTSTEEEAEEAAEAALSTV 235

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI E+L  
Sbjct: 236 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLQAMMLAISASPATIAEVLEM 295

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A+KI      I  +VDG +  + + +    +     +EE+    +  +   T++LE+LK 
Sbjct: 296 ANKIRAGTDPISSVVDGFVAADEADDYVAEEDFDEFDEEEDDDGNGGSKALTKKLEELKN 355

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L+KF  +   FDKMRKA++K+GY S +Y KA   IS +++ +RFT K+IEKLCD LR+
Sbjct: 356 QALVKFDALQLDFDKMRKAYDKDGYKSPAYNKAQEAISGQLMTVRFTVKTIEKLCDLLRS 415

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ + + E+++ +IVV++CGMP+ +FIK FP N +NL W +NE      Y+ ++ RN+P
Sbjct: 416 QVDDIRRFERELRKIVVDRCGMPQEYFIKSFPPNILNLEWAENEIAANKPYSAVMSRNLP 475

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
           +I+ELQQKL +LQT  V+P++DL+ INR+M  GE  +R+AKREM EANLRLVISIAKKYT
Sbjct: 476 AIQELQQKLTDLQTKAVVPIDDLKQINRRMNEGEASSREAKREMIEANLRLVISIAKKYT 535

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 536 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 595

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++R+SRQ LQE G EPD   +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 596 MIETINKMNRLSRQHLQEFGFEPDAPSLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDD 655

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP +AA+ + +R VV+DIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 656 DSHLGDFIEDTNNTAPIEAAMQSGLRDVVRDILDSLTPREAKVLRMRFGIEMSTDHTLEE 715

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKA+RKL+
Sbjct: 716 VGKQFDVTRERIRQIEAKAIRKLK 739


>gi|160900477|ref|YP_001566059.1| RNA polymerase sigma 70 subunit RpoD [Delftia acidovorans SPH-1]
 gi|160366061|gb|ABX37674.1| RNA polymerase, sigma 70 subunit, RpoD [Delftia acidovorans SPH-1]
          Length = 808

 Score =  749 bits (1934), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/619 (60%), Positives = 471/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K LIKLGK RGYLT SEIND LP+ ++D E +E +I    
Sbjct: 188  FGLDETVLTEEEMSTRRQRLKALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLN 247

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N       EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 248  DMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 307

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  +++I + ++ I  IVDG 
Sbjct: 308  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVDGF 367

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++ N + +    +     +EE        +   T++LE+LK E+L +F  +  +FDKM K
Sbjct: 368  VNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKNEALRRFDAMRENFDKMHK 427

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +YIK    ++ E++ IRFTAK+IEKLCD +R Q++ V + E+++ +I+V+
Sbjct: 428  VYDKEGYGTPTYIKVQKALTEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVD 487

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FI  FP N +NL WV  +      ++ +L RNIP ++ELQQ LI+LQ+ +V+
Sbjct: 488  KCGMPQETFIAQFPPNLLNLQWVVQQVAAGKPWSNVLERNIPPVQELQQNLIDLQSRVVV 547

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 548  PLDELKRINKRMNDGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 607

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 608  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 667

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 668  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPVD 727

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 728  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 787

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 788  ALRKLKHPSRSDKLRSFID 806



 Score =  739 bits (1908), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/624 (59%), Positives = 469/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K LIKLGK RGYLT SEIND L
Sbjct: 170 KPLRMKISKAKERALMKEFGLDETVLTEEEMSTRRQRLKALIKLGKTRGYLTHSEINDHL 229

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 230 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTV 289

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 290 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILAM 349

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           +++I + ++ I  IVDG ++ N + +    +     +EE        +   T++LE+LK 
Sbjct: 350 SEEIREGKVVISTIVDGFVNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKN 409

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +  +FDKM K ++KEGY + +YIK    ++ E++ IRFTAK+IEKLCD +R 
Sbjct: 410 EALRRFDAMRENFDKMHKVYDKEGYGTPTYIKVQKALTEELMTIRFTAKTIEKLCDLVRA 469

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++ +I+V+KCGMP+  FI  FP N +NL WV  +      ++ +L RNIP
Sbjct: 470 QVDDVRKKERELRKIIVDKCGMPQETFIAQFPPNLLNLQWVVQQVAAGKPWSNVLERNIP 529

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI+LQ+ +V+PL++L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 530 PVQELQQNLIDLQSRVVVPLDELKRINKRMNDGERASRDAKKEMIEANLRLVISIAKKYT 589

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 590 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 649

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 650 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 709

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 710 DSHLGDFIEDTNNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 769

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 770 VGKQFDVTRERIRQIEAKALRKLK 793


>gi|120610093|ref|YP_969771.1| RpoD family RNA polymerase sigma factor [Acidovorax citrulli AAC00-1]
 gi|120588557|gb|ABM31997.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax citrulli AAC00-1]
          Length = 781

 Score =  746 bits (1927), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/619 (60%), Positives = 472/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 161  FGLDDTVLSEEDLAKRRSRLKALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLN 220

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+T         EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 221  DMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 280

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 281  GTVELLTREGEIEIAKRIEGGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVDGF 340

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F N+   F+KM K
Sbjct: 341  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKNEALRRFDNLRGLFEKMHK 400

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA + IS E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 401  IYDKEGYGTPAYMKAQHAISAELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVD 460

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ +L RNIP ++ELQQ+L++LQ+ +V+
Sbjct: 461  KCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVLARNIPPVQELQQRLMDLQSRVVV 520

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 521  PLSELKDINKRMNEGESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 580

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 581  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 640

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP D
Sbjct: 641  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPID 700

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 701  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 760

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 761  ALRKLKHPSRSDKLRSFID 779



 Score =  737 bits (1902), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/624 (59%), Positives = 470/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 143 KPLRMKISKAKERALMKEFGLDDTVLSEEDLAKRRSRLKALITLGKTRGYLTQVEISDHL 202

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL  +N+T         EE  EAALSTV
Sbjct: 203 PDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTV 262

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL  
Sbjct: 263 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLQAMMEAISASPATIAEILAM 322

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 323 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKN 382

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F N+   F+KM K ++KEGY + +Y+KA + IS E++ IRFTAK+IEKLCD +R 
Sbjct: 383 EALRRFDNLRGLFEKMHKIYDKEGYGTPAYMKAQHAISAELMTIRFTAKTIEKLCDMVRA 442

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ +L RNIP
Sbjct: 443 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVLARNIP 502

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ+L++LQ+ +V+PL++L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 503 PVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASRDAKKEMIEANLRLVISIAKKYT 562

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 563 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 622

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 623 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 682

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 683 DSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 742

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 743 VGKQFDVTRERIRQIEAKALRKLK 766


>gi|56477911|ref|YP_159500.1| RNA polymerase sigma factor RpoD [Aromatoleum aromaticum EbN1]
 gi|56313954|emb|CAI08599.1| DNA-dependent RNA polymerase sigma subunits (Sigma70/32) [Aromatoleum
            aromaticum EbN1]
          Length = 663

 Score =  746 bits (1926), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/620 (60%), Positives = 468/620 (75%), Gaps = 23/620 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 43   RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIRVFDEAPAAEDL 102

Query: 890  MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++S+       E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 103  LMSDAVPSSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 162

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+GL+ M+ AIS+CPTTI E+L   DK++++E++IDE++DGLID N +          
Sbjct: 163  RIEDGLRHMVQAISACPTTIAEMLEITDKVARDEMRIDELIDGLIDPNAAQAAEASAAET 222

Query: 1006 NNNEEKI-----------------LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
             ++E                      + ++A+ +T  L +LK ++L++F+ I    ++  
Sbjct: 223  ADDERAADDEVESEDGGDDDDESDEDKEAAANAAT--LLQLKNDALVRFAIIRELHERKM 280

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
             A    G    SY+     IS E+L IRFTAK+IE+LCD++R+ + QV   E+ IL++ V
Sbjct: 281  AALATVGSQDRSYLDLQQQISGELLNIRFTAKAIERLCDSVRHMVEQVRGHERHILQLCV 340

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            ++ GMPR HFIKVFP  EI+L+W+ +E     +Y   L R  P++ E QQKLI+LQT I 
Sbjct: 341  DRAGMPRQHFIKVFPGREIDLDWLKDEIGAGKNYAEGLMRVHPAVLEEQQKLIDLQTRIG 400

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 401  IPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 460

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 461  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 520

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+  LAP+
Sbjct: 521  ETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLAPA 580

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA+ +S+R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 581  DAAMYSSLRDATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 640

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR  +L+ FL+
Sbjct: 641  KALRKLRHPSRSERLRSFLD 660



 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/607 (60%), Positives = 458/607 (75%), Gaps = 23/607 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 43  RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIRVFDEAPAAEDL 102

Query: 100 MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++S+       E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 103 LMSDAVPSSVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 162

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+GL+ M+ AIS+CPTTI E+L   DK++++E++IDE++DGLID N +          
Sbjct: 163 RIEDGLRHMVQAISACPTTIAEMLEITDKVARDEMRIDELIDGLIDPNAAQAAEASAAET 222

Query: 216 NNNEEKI-----------------LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
            ++E                      + ++A+ +T  L +LK ++L++F+ I    ++  
Sbjct: 223 ADDERAADDEVESEDGGDDDDESDEDKEAAANAAT--LLQLKNDALVRFAIIRELHERKM 280

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
            A    G    SY+     IS E+L IRFTAK+IE+LCD++R+ + QV   E+ IL++ V
Sbjct: 281 AALATVGSQDRSYLDLQQQISGELLNIRFTAKAIERLCDSVRHMVEQVRGHERHILQLCV 340

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           ++ GMPR HFIKVFP  EI+L+W+ +E     +Y   L R  P++ E QQKLI+LQT I 
Sbjct: 341 DRAGMPRQHFIKVFPGREIDLDWLKDEIGAGKNYAEGLMRVHPAVLEEQQKLIDLQTRIG 400

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 401 IPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 460

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 461 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 520

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+  LAP+
Sbjct: 521 ETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLAPA 580

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA+ +S+R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 581 DAAMYSSLRDATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 640

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 641 KALRKLR 647


>gi|326316262|ref|YP_004233934.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax avenae subsp. avenae
            ATCC 19860]
 gi|323373098|gb|ADX45367.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax avenae subsp.
            avenae ATCC 19860]
          Length = 780

 Score =  746 bits (1926), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/619 (60%), Positives = 472/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 160  FGLDDTVLSEEDLAKRRSRLKALITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVTMLN 219

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+T         EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 220  DMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 279

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 280  GTVELLTREGEIEIAKRIEGGLQAMMEAISASPATIAEILAMGEEIREGKVVISTIVDGF 339

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F N+   F+KM K
Sbjct: 340  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKNEALRRFDNLRGLFEKMHK 399

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA + IS E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 400  IYDKEGYGTPAYMKAQHAISAELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVD 459

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ +L RNIP ++ELQQ+L++LQ+ +V+
Sbjct: 460  KCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVLARNIPPVQELQQRLMDLQSRVVV 519

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 520  PLSELKDINKRMNEGESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 579

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 580  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 639

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP D
Sbjct: 640  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPID 699

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 700  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 759

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 760  ALRKLKHPSRSDKLRSFID 778



 Score =  736 bits (1901), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/624 (59%), Positives = 470/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 142 KPLRMKISKAKERALMKEFGLDDTVLSEEDLAKRRSRLKALITLGKTRGYLTQVEISDHL 201

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL  +N+T         EE  EAALSTV
Sbjct: 202 PDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTV 261

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL  
Sbjct: 262 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLQAMMEAISASPATIAEILAM 321

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 322 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKN 381

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F N+   F+KM K ++KEGY + +Y+KA + IS E++ IRFTAK+IEKLCD +R 
Sbjct: 382 EALRRFDNLRGLFEKMHKIYDKEGYGTPAYMKAQHAISAELMTIRFTAKTIEKLCDMVRA 441

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ +L RNIP
Sbjct: 442 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVLARNIP 501

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ+L++LQ+ +V+PL++L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 502 PVQELQQRLMDLQSRVVVPLSELKDINKRMNEGESASRDAKKEMIEANLRLVISIAKKYT 561

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 562 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 621

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 622 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 681

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 682 DSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 741

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 742 VGKQFDVTRERIRQIEAKALRKLK 765


>gi|217969610|ref|YP_002354844.1| RNA polymerase sigma factor RpoD [Thauera sp. MZ1T]
 gi|217506937|gb|ACK53948.1| RNA polymerase, sigma 70 subunit, RpoD [Thauera sp. MZ1T]
          Length = 666

 Score =  746 bits (1925), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/620 (60%), Positives = 468/620 (75%), Gaps = 21/620 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 44   RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIQVYDEAPAAEDL 103

Query: 890  MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++S+  + +  E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 104  LMSDSVATNVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 163

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+GLK M+ AIS+CPTTI E+L   D+I+ ++ KIDE+VDGLID N  S        +
Sbjct: 164  RIEDGLKHMVQAISACPTTIAEMLGIVDRIAADDAKIDELVDGLIDPNAGSAEEAAAEEE 223

Query: 1006 NNNEEKILIES-----------------SSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
            + +E+    E                  S+   +   L +LK ++L +F  I   ++K  
Sbjct: 224  SADEDTEAEEDEGAEDEDEGDDEEDSAESAERANAASLLQLKNDALARFDVIRGLYEKKM 283

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
            +A EK G    SY+     IS+E+L IRFTAK+IEKLCD++R+ + QV   E+QIL++ V
Sbjct: 284  QALEKRGSQDLSYLALQQQISDELLNIRFTAKAIEKLCDSVRHMVEQVRSHERQILQLCV 343

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            ++ GMPR HFIKVFP  E+NL+W+ +E     +Y   L R  P++ E QQKLI+LQ  I 
Sbjct: 344  DRAGMPRQHFIKVFPGQEVNLDWLKDEIAAGKNYADGLMRIHPAVLEEQQKLIDLQDRIG 403

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 404  IPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 463

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 464  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 523

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP+
Sbjct: 524  ETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLAPA 583

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            +AA+ + +R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 584  EAAMYSGLRDATCEVLDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 643

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR  KL+ FL+
Sbjct: 644  KALRKLRHPSRSEKLRSFLD 663



 Score =  729 bits (1881), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/607 (60%), Positives = 458/607 (75%), Gaps = 21/607 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 44  RTRLKTLITLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIQVYDEAPAAEDL 103

Query: 100 MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++S+  + +  E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 104 LMSDSVATNVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 163

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+GLK M+ AIS+CPTTI E+L   D+I+ ++ KIDE+VDGLID N  S        +
Sbjct: 164 RIEDGLKHMVQAISACPTTIAEMLGIVDRIAADDAKIDELVDGLIDPNAGSAEEAAAEEE 223

Query: 216 NNNEEKILIES-----------------SSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
           + +E+    E                  S+   +   L +LK ++L +F  I   ++K  
Sbjct: 224 SADEDTEAEEDEGAEDEDEGDDEEDSAESAERANAASLLQLKNDALARFDVIRGLYEKKM 283

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
           +A EK G    SY+     IS+E+L IRFTAK+IEKLCD++R+ + QV   E+QIL++ V
Sbjct: 284 QALEKRGSQDLSYLALQQQISDELLNIRFTAKAIEKLCDSVRHMVEQVRSHERQILQLCV 343

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           ++ GMPR HFIKVFP  E+NL+W+ +E     +Y   L R  P++ E QQKLI+LQ  I 
Sbjct: 344 DRAGMPRQHFIKVFPGQEVNLDWLKDEIAAGKNYADGLMRIHPAVLEEQQKLIDLQDRIG 403

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           +PL +L+DINR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 404 IPLKELKDINRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 463

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 464 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 523

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   LAP+
Sbjct: 524 ETGQEPDPATLAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDTATLAPA 583

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           +AA+ + +R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 584 EAAMYSGLRDATCEVLDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 643

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 644 KALRKLR 650


>gi|333913225|ref|YP_004486957.1| RNA polymerase sigma-70 subunit RpoD [Delftia sp. Cs1-4]
 gi|333743425|gb|AEF88602.1| RNA polymerase, sigma 70 subunit, RpoD [Delftia sp. Cs1-4]
          Length = 813

 Score =  745 bits (1924), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/619 (59%), Positives = 470/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K LIKLGK RGYLT SEIND LP+ ++D E +E +I    
Sbjct: 193  FGLDETVLTEEEMSTRRQRLKALIKLGKTRGYLTHSEINDHLPDKLVDAETLEVVISMLN 252

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N       EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 253  DMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 312

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  +++I + ++ I  IVDG 
Sbjct: 313  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILAMSEEIREGKVVISTIVDGF 372

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++ N + +    +     +EE        +   T++LE+LK E+L +F  +  +FDKM K
Sbjct: 373  VNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKNEALRRFDAMRENFDKMHK 432

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++K+GY +  Y+K    ++ E++ IRFTAK+IEKLCD +R Q++ V + E+++ +I+V+
Sbjct: 433  VYDKDGYGTPVYMKVQKALTEELMTIRFTAKTIEKLCDLVRAQVDDVRKKERELRKIIVD 492

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FI  FP N +NL WV  +      ++ +L RNIP ++ELQQ LI+LQ+ +V+
Sbjct: 493  KCGMPQETFIAQFPPNLLNLQWVVQQVAAGKPWSNVLERNIPPVQELQQNLIDLQSRVVV 552

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 553  PLDELKRINKRMNDGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 612

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 613  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 672

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 673  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNNTAPVD 732

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 733  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 792

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 793  ALRKLKHPSRSDKLRSFID 811



 Score =  736 bits (1899), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/624 (59%), Positives = 468/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K LIKLGK RGYLT SEIND L
Sbjct: 175 KPLRMKISKAKERALMKEFGLDETVLTEEEMSTRRQRLKALIKLGKTRGYLTHSEINDHL 234

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 235 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNTGQSATTEEEAEEEAEAALSTV 294

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 295 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILAM 354

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           +++I + ++ I  IVDG ++ N + +    +     +EE        +   T++LE+LK 
Sbjct: 355 SEEIREGKVVISTIVDGFVNANENDDYVAEEDFDEYDEEDDDDGKGGSKALTKKLEELKN 414

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +  +FDKM K ++K+GY +  Y+K    ++ E++ IRFTAK+IEKLCD +R 
Sbjct: 415 EALRRFDAMRENFDKMHKVYDKDGYGTPVYMKVQKALTEELMTIRFTAKTIEKLCDLVRA 474

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++ +I+V+KCGMP+  FI  FP N +NL WV  +      ++ +L RNIP
Sbjct: 475 QVDDVRKKERELRKIIVDKCGMPQETFIAQFPPNLLNLQWVVQQVAAGKPWSNVLERNIP 534

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI+LQ+ +V+PL++L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 535 PVQELQQNLIDLQSRVVVPLDELKRINKRMNDGERASRDAKKEMIEANLRLVISIAKKYT 594

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 595 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 654

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 655 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 714

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 715 DSHLGDFIEDTNNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 774

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 775 VGKQFDVTRERIRQIEAKALRKLK 798


>gi|121595443|ref|YP_987339.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|120607523|gb|ABM43263.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax sp. JS42]
          Length = 797

 Score =  744 bits (1922), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/619 (60%), Positives = 470/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 177  FGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLG 236

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+T         EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 237  DMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 296

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ I  +VDG 
Sbjct: 297  GKVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVDGF 356

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F  +   F+KM K
Sbjct: 357  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKNEALRRFDTLRALFEKMHK 416

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++K+GY   +Y+K  + IS E++ IRFTAK+IEKLCD +R Q++ V ++E+++  I+V+
Sbjct: 417  IYDKDGYGGPAYMKVQHEISAELMTIRFTAKTIEKLCDMVRAQVDDVRKMERELRRIIVD 476

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQQKLI+LQ  +V+
Sbjct: 477  KCGMPQETFIKEFPANLLNLQWVEKQAAAGKPWSAVMQRNIPPIQELQQKLIDLQARVVV 536

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L++IN++M AGE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 537  PLSELKEINKRMNAGEASSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 596

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 597  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 656

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 657  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPVD 716

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 717  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 776

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 777  ALRKLKHPSRSDKLRSFID 795



 Score =  735 bits (1897), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/624 (59%), Positives = 468/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 159 KPLRMKISKAKERALMKEFGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHL 218

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL  +N+T         EE  EAALSTV
Sbjct: 219 PDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTV 278

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 279 DSEFGRTTDPVRMYMREMGKVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNM 338

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  +VDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 339 GEEIREGKVVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKN 398

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +   F+KM K ++K+GY   +Y+K  + IS E++ IRFTAK+IEKLCD +R 
Sbjct: 399 EALRRFDTLRALFEKMHKIYDKDGYGGPAYMKVQHEISAELMTIRFTAKTIEKLCDMVRA 458

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V ++E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 459 QVDDVRKMERELRRIIVDKCGMPQETFIKEFPANLLNLQWVEKQAAAGKPWSAVMQRNIP 518

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQQKLI+LQ  +V+PL++L++IN++M AGE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 519 PIQELQQKLIDLQARVVVPLSELKEINKRMNAGEASSRDAKKEMIEANLRLVISIAKKYT 578

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 579 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 638

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 639 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 698

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 699 DSHLGDFIEDSNNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 758

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 759 VGKQFDVTRERIRQIEAKALRKLK 782


>gi|30248253|ref|NP_840323.1| RNA polymerase sigma factor RpoD [Nitrosomonas europaea ATCC 19718]
 gi|30180138|emb|CAD84140.1| DNA-dependent RNA polymerase sigma subunits (sigma70/32)
            [Nitrosomonas europaea ATCC 19718]
          Length = 751

 Score =  743 bits (1918), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/622 (59%), Positives = 471/622 (75%), Gaps = 16/622 (2%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +  +S  +IE  R + K LI  GKERGYLT+SEIND LP+D++D + IESII     M I
Sbjct: 131  VSVSSDNDIELRRMRLKKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGI 190

Query: 878  SVSEHVLDTETLMLSNITS---DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            SV +   D E L++S+  +   D+DV E  EAALS+VDS+FGRT DP++MYMREMGSVEL
Sbjct: 191  SVHDEAPDAEALLMSDAATAVTDEDVVEEAEAALSSVDSEFGRTTDPVRMYMREMGSVEL 250

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+ EIEIAKRIE+GL+ MI AIS+CPT I  IL  A  +    ++ DE+VDG +D + 
Sbjct: 251  LTRESEIEIAKRIEDGLRHMIQAISACPTIIENILELAADVENGRLRADELVDGFLDDDT 310

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-------KLKYESLIKFSNISFHFDKM 1047
                  I G K  +EE +  +  S D   EQ+        K+K E L +F+ I   +D M
Sbjct: 311  DE----IMG-KEMSEESLDQDFDSEDGEDEQVAAASADMLKMKAEVLERFAVIRQTYDGM 365

Query: 1048 RKAF-EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            +K   +K+G   + Y +    IS E++ +RF+AK +EKLCDT R+ +N +   E++I E+
Sbjct: 366  KKIINKKDGRQDKKYKQLQEKISTELMAMRFSAKMVEKLCDTQRDIVNDIRNCERKIAEL 425

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V + GMPR +FIK FP NE +++W+ +E +    Y+  L    P++ E QQK++ LQ  
Sbjct: 426  CVTRAGMPRNYFIKAFPGNETDIDWISSEVESGQPYSQSLEHFRPAVMEQQQKMLELQKQ 485

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              +P+ +L++INR+M  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 486  AGIPIKELKEINRRMTTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 545

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQI
Sbjct: 546  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 605

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG EP+P+V+A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED + + 
Sbjct: 606  LQETGQEPEPAVLAEKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDASTME 665

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P+DAA+ A +R+V KD+L+SLTPRE+KVLRMRFGIEM++DHTLEEVG+QFDVTRERIRQI
Sbjct: 666  PADAAVYAGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQI 725

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHP+R  +L+ FL+
Sbjct: 726  EAKALRKLRHPARSDRLRSFLD 747



 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/645 (57%), Positives = 479/645 (74%), Gaps = 22/645 (3%)

Query: 4   INKKTKIKNKKTKETLLKNAFS----FDIKSNSREEIENLRKKFKILIKLGKERGYLTFS 59
           +++KT++ +K+ K TL +   +      +  +S  +IE  R + K LI  GKERGYLT+S
Sbjct: 104 VSEKTRV-SKRNKSTLSEKQITDLSESAVSVSSDNDIELRRMRLKKLIMQGKERGYLTYS 162

Query: 60  EINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS---DDDVEEATEA 116
           EIND LP+D++D + IESII     M ISV +   D E L++S+  +   D+DV E  EA
Sbjct: 163 EINDHLPDDMLDADQIESIISMINDMGISVHDEAPDAEALLMSDAATAVTDEDVVEEAEA 222

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
           ALS+VDS+FGRT DP++MYMREMGSVELLTR+ EIEIAKRIE+GL+ MI AIS+CPT I 
Sbjct: 223 ALSSVDSEFGRTTDPVRMYMREMGSVELLTRESEIEIAKRIEDGLRHMIQAISACPTIIE 282

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            IL  A  +    ++ DE+VDG +D +       I G K  +EE +  +  S D   EQ+
Sbjct: 283 NILELAADVENGRLRADELVDGFLDDDTDE----IMG-KEMSEESLDQDFDSEDGEDEQV 337

Query: 237 E-------KLKYESLIKFSNISFHFDKMRKAF-EKEGYNSESYIKAHNNISNEMLGIRFT 288
                   K+K E L +F+ I   +D M+K   +K+G   + Y +    IS E++ +RF+
Sbjct: 338 AAASADMLKMKAEVLERFAVIRQTYDGMKKIINKKDGRQDKKYKQLQEKISTELMAMRFS 397

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
           AK +EKLCDT R+ +N +   E++I E+ V + GMPR +FIK FP NE +++W+ +E + 
Sbjct: 398 AKMVEKLCDTQRDIVNDIRNCERKIAELCVTRAGMPRNYFIKAFPGNETDIDWISSEVES 457

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              Y+  L    P++ E QQK++ LQ    +P+ +L++INR+M  GE KAR+AKREMTEA
Sbjct: 458 GQPYSQSLEHFRPAVMEQQQKMLELQKQAGIPIKELKEINRRMTTGEAKARRAKREMTEA 517

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 518 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 577

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQILQETG EP+P+V+A KMEMPEEKIRKI+KI+K
Sbjct: 578 IADQARTIRIPVHMIETINKMNRISRQILQETGQEPEPAVLAEKMEMPEEKIRKILKISK 637

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED + + P+DAA+ A +R+V KD+L+SLTPRE+KVLRMR
Sbjct: 638 EPISMETPIGDDEDSHLGDFIEDASTMEPADAAVYAGLRTVTKDVLDSLTPREAKVLRMR 697

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           FGIEM++DHTLEEVG+QFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 698 FGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPARSDRL 742


>gi|222111657|ref|YP_002553921.1| RNA polymerase sigma-70 subunit RpoD [Acidovorax ebreus TPSY]
 gi|221731101|gb|ACM33921.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax ebreus TPSY]
          Length = 801

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/619 (59%), Positives = 470/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 181  FGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLG 240

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+T         EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 241  DMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 300

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ I  +VDG 
Sbjct: 301  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVDGF 360

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F  +   F+KM K
Sbjct: 361  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKNEALRRFDTLRALFEKMHK 420

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++K+GY   +Y+K  + IS E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 421  IYDKDGYGGPAYMKVQHEISAELMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVD 480

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQQKL++LQ  +V+
Sbjct: 481  KCGMPQETFIKDFPANLLNLQWVEKQAAAGKPWSAVMQRNIPPIQELQQKLMDLQARVVV 540

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL++L++IN++M AGE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 541  PLSELKEINKRMNAGEASSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 600

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 601  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 660

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED +  AP D
Sbjct: 661  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSSNTAPVD 720

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 721  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 780

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 781  ALRKLKHPSRSDKLRSFID 799



 Score =  730 bits (1885), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/624 (59%), Positives = 468/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 163 KPLRMKISKAKERALMKEFGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHL 222

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDV----EEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL  +N+T         EE  EAALSTV
Sbjct: 223 PDKLVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNNVTPTATTVEEAEEEAEAALSTV 282

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL  
Sbjct: 283 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNM 342

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  +VDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 343 GEEIREGKVVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKN 402

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +   F+KM K ++K+GY   +Y+K  + IS E++ IRFTAK+IEKLCD +R 
Sbjct: 403 EALRRFDTLRALFEKMHKIYDKDGYGGPAYMKVQHEISAELMTIRFTAKTIEKLCDMVRA 462

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 463 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPANLLNLQWVEKQAAAGKPWSAVMQRNIP 522

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQQKL++LQ  +V+PL++L++IN++M AGE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 523 PIQELQQKLMDLQARVVVPLSELKEINKRMNAGEASSRDAKKEMIEANLRLVISIAKKYT 582

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 583 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 642

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 643 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 702

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED +  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 703 DSHLGDFIEDSSNTAPVDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 762

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 763 VGKQFDVTRERIRQIEAKALRKLK 786


>gi|398804564|ref|ZP_10563557.1| RNA polymerase sigma factor, sigma-70 family [Polaromonas sp. CF318]
 gi|398093561|gb|EJL83939.1| RNA polymerase sigma factor, sigma-70 family [Polaromonas sp. CF318]
          Length = 820

 Score =  740 bits (1910), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/619 (59%), Positives = 470/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 200  FGLDETVLSEEDMLKRRLRLKTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVVNMLN 259

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N    + ++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 260  DMGVAVYEQAPDAETLLLNNTGPTVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 319

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+   ++I + +I I  +VDG 
Sbjct: 320  GTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRLGEEIREGKIVISTVVDGF 379

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F  I+  F+K+ K
Sbjct: 380  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKKEALSRFDKIAALFEKVHK 439

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S+E++ +RFTAK+IEKLCD LR Q+  V + E+++  I+V 
Sbjct: 440  TYDKEGYGTPTYVKAQKALSDELMTVRFTAKTIEKLCDMLRGQVLDVRKKERELRRIIVE 499

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      +++++ RN+P I+ELQ KL  LQ  +V+
Sbjct: 500  KCGMPQEVFIKDFPPNLLNLKWVEKQVAAGKPWSVVMARNVPPIQELQTKLAELQARVVV 559

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 560  PLAQLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 619

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 620  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 679

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 680  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSANTAPLE 739

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 740  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 799

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 800  ALRKLKHPSRSDKLRSFID 818



 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/624 (58%), Positives = 468/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D L
Sbjct: 182 KPLRMKISKAKERALMKEFGLDETVLSEEDMLKRRLRLKTLIKLGKTRGYLTHGEISDHL 241

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL+L+N    + ++++ EE  EAALSTV
Sbjct: 242 PDKLVDAETLEVVVNMLNDMGVAVYEQAPDAETLLLNNTGPTVATEEEAEEEAEAALSTV 301

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+  
Sbjct: 302 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRL 361

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + +I I  +VDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 362 GEEIREGKIVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKK 421

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  I+  F+K+ K ++KEGY + +Y+KA   +S+E++ +RFTAK+IEKLCD LR 
Sbjct: 422 EALSRFDKIAALFEKVHKTYDKEGYGTPTYVKAQKALSDELMTVRFTAKTIEKLCDMLRG 481

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q+  V + E+++  I+V KCGMP+  FIK FP N +NL WV+ +      +++++ RN+P
Sbjct: 482 QVLDVRKKERELRRIIVEKCGMPQEVFIKDFPPNLLNLKWVEKQVAAGKPWSVVMARNVP 541

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQ KL  LQ  +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 542 PIQELQTKLAELQARVVVPLAQLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYT 601

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 602 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 661

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++R+SRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 662 MIETINKMNRLSRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 721

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 722 DSHLGDFIEDSANTAPLEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 781

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 782 VGKQFDVTRERIRQIEAKALRKLK 805


>gi|337280116|ref|YP_004619588.1| RNA polymerase sigma-70 factor [Ramlibacter tataouinensis TTB310]
 gi|334731193|gb|AEG93569.1| Candidate RNA polymerase sigma-70 factor [Ramlibacter tataouinensis
            TTB310]
          Length = 792

 Score =  739 bits (1909), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/619 (59%), Positives = 473/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    + EE+   R++ K LI LGK RGYLT +EI D LPE +++ E +E ++    
Sbjct: 172  FGLDETILTEEEMLKRRQRLKTLITLGKTRGYLTHAEITDHLPEKLVEAETLEVVVTMLN 231

Query: 874  YMDISVSEHVLDTETLMLSNITSD----DDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L+L+N T      ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 232  DLGVAVYEQTPDAEMLLLNNTTPTVATAEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 291

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL  A  I + ++ I  IVDG 
Sbjct: 292  GTVELLTREGEIEIAKRIEAGLQAMMEAISASPATIAEILRMAADIREGKVVISSIVDGF 351

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     + +     +  +   T++LE+LK ++L +F  I+  F+K+ K
Sbjct: 352  SNPNEADDYVAEEDFDEFDADDDDDGNGGSKALTKKLEELKAQALERFDRIAGLFEKVHK 411

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 412  VYDKEGYGTPAYNKAQQALSEELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 471

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQQKL++LQ+ +V+
Sbjct: 472  KCGMPQETFIKEFPPNLLNLKWVEKQAAAGKPWSTVIARNIPPIQELQQKLMDLQSRVVV 531

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L++IN++M  GE  +R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 532  PLPELKEINKRMNEGEASSREAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 591

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 592  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 651

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 652  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTGNTAPIE 711

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 712  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 771

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 772  ALRKLKHPSRSDKLRSFID 790



 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/624 (58%), Positives = 471/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    + EE+   R++ K LI LGK RGYLT +EI D L
Sbjct: 154 KPLRMKISKAKERALMKEFGLDETILTEEEMLKRRQRLKTLITLGKTRGYLTHAEITDHL 213

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSD----DDVEEATEAALSTV 121
           PE +++ E +E ++     + ++V E   D E L+L+N T      ++ EE  EAALSTV
Sbjct: 214 PEKLVEAETLEVVVTMLNDLGVAVYEQTPDAEMLLLNNTTPTVATAEEAEEEAEAALSTV 273

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL+ M+ AIS+ P TI EIL  
Sbjct: 274 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLQAMMEAISASPATIAEILRM 333

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A  I + ++ I  IVDG  + N + +    +     + +     +  +   T++LE+LK 
Sbjct: 334 AADIREGKVVISSIVDGFSNPNEADDYVAEEDFDEFDADDDDDGNGGSKALTKKLEELKA 393

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  I+  F+K+ K ++KEGY + +Y KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 394 QALERFDRIAGLFEKVHKVYDKEGYGTPAYNKAQQALSEELMTIRFTAKTIEKLCDMVRG 453

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 454 QVDDVRKKERELRRIIVDKCGMPQETFIKEFPPNLLNLKWVEKQAAAGKPWSTVIARNIP 513

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQQKL++LQ+ +V+PL +L++IN++M  GE  +R+AK+EM EANLRLVISIAKKYT
Sbjct: 514 PIQELQQKLMDLQSRVVVPLPELKEINKRMNEGEASSREAKKEMIEANLRLVISIAKKYT 573

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 574 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 633

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 634 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 693

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 694 DSHLGDFIEDTGNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 753

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 754 VGKQFDVTRERIRQIEAKALRKLK 777


>gi|91788957|ref|YP_549909.1| sigma 70 (RpoD) [Polaromonas sp. JS666]
 gi|91698182|gb|ABE45011.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas sp. JS666]
          Length = 784

 Score =  738 bits (1904), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/619 (59%), Positives = 469/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 164  FGLDETVLSEEDMLKRRMRLKTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVVNMLN 223

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N    + ++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 224  DMGVAVYEQAPDAETLLLNNTGPTVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 283

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+   ++I + +I I  +VDG 
Sbjct: 284  GTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRLGEEIREGKIVISTVVDGF 343

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F  I+  F+K+ K
Sbjct: 344  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKKEALSRFDKIASLFEKVHK 403

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S+E++ +RFTAK+IEKLCD LR Q+  V + E+++  I+V 
Sbjct: 404  TYDKEGYGTPTYVKAQKALSDELMTVRFTAKTIEKLCDMLRGQVLDVRKKERELRRIIVE 463

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQ KL  LQ  +V+
Sbjct: 464  KCGMPQETFIKDFPPNLLNLKWVEKQVASGKPWSTVMARNIPPIQELQTKLAELQARVVV 523

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 524  PLGQLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 583

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 584  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 643

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 644  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSANTAPLE 703

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 704  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 763

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 764  ALRKLKHPSRSDKLRSFID 782



 Score =  728 bits (1879), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/624 (58%), Positives = 467/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D L
Sbjct: 146 KPLRMKISKAKERALMKEFGLDETVLSEEDMLKRRMRLKTLIKLGKTRGYLTHGEISDHL 205

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL+L+N    + ++++ EE  EAALSTV
Sbjct: 206 PDKLVDAETLEVVVNMLNDMGVAVYEQAPDAETLLLNNTGPTVATEEEAEEEAEAALSTV 265

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+  
Sbjct: 266 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRL 325

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + +I I  +VDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 326 GEEIREGKIVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKK 385

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  I+  F+K+ K ++KEGY + +Y+KA   +S+E++ +RFTAK+IEKLCD LR 
Sbjct: 386 EALSRFDKIASLFEKVHKTYDKEGYGTPTYVKAQKALSDELMTVRFTAKTIEKLCDMLRG 445

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q+  V + E+++  I+V KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 446 QVLDVRKKERELRRIIVEKCGMPQETFIKDFPPNLLNLKWVEKQVASGKPWSTVMARNIP 505

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQ KL  LQ  +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 506 PIQELQTKLAELQARVVVPLGQLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYT 565

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 566 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 625

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++R+SRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 626 MIETINKMNRLSRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 685

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 686 DSHLGDFIEDSANTAPLEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 745

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 746 VGKQFDVTRERIRQIEAKALRKLK 769


>gi|399114901|emb|CCG17697.1| RNA polymerase sigma factor 70 [Taylorella equigenitalis 14/56]
          Length = 902

 Score =  738 bits (1904), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/622 (60%), Positives = 475/622 (76%), Gaps = 8/622 (1%)

Query: 811  KNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 869
            K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES++
Sbjct: 283  KGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMV 342

Query: 870  KTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
             T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++MYM
Sbjct: 343  STLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYM 402

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+EIV
Sbjct: 403  REMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIV 462

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
            DGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   FDK
Sbjct: 463  DGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAFDK 518

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK +L +
Sbjct: 519  MKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMLSV 578

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+ +
Sbjct: 579  CVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLEKE 638

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
            ++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 639  VILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 698

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQI
Sbjct: 699  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQI 758

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+
Sbjct: 759  LQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLS 818

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQI
Sbjct: 819  PEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQI 878

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR  KLK FLE
Sbjct: 879  EAKALRKLRHPSRADKLKSFLE 900



 Score =  717 bits (1852), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/617 (60%), Positives = 468/617 (75%), Gaps = 9/617 (1%)

Query: 21  KNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 79
           K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES++
Sbjct: 283 KGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMV 342

Query: 80  KTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 136
            T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++MYM
Sbjct: 343 STLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYM 402

Query: 137 REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
           REMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+EIV
Sbjct: 403 REMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIV 462

Query: 197 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
           DGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   FDK
Sbjct: 463 DGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAFDK 518

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK +L +
Sbjct: 519 MKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMLSV 578

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+ +
Sbjct: 579 CVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLEKE 638

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
           ++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 639 VILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 698

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQI
Sbjct: 699 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQI 758

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+
Sbjct: 759 LQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLS 818

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQI
Sbjct: 819 PEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQI 878

Query: 617 EAKALRKLR-PLAHDWL 632
           EAKALRKLR P   D L
Sbjct: 879 EAKALRKLRHPSRADKL 895


>gi|407938354|ref|YP_006853995.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. KKS102]
 gi|407896148|gb|AFU45357.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. KKS102]
          Length = 792

 Score =  737 bits (1903), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/619 (59%), Positives = 475/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E+++  R++ K LIKLGK RGYLT  EIND LP+ ++D E +E++I T  
Sbjct: 172  FGLDETVLSEEDMQKRRQRLKALIKLGKTRGYLTHVEINDHLPDKLVDAETLEAVITTLN 231

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++      ++++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 232  DLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 291

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 292  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVDGF 351

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 352  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRELFEKVHK 411

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +YIKA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 412  VYDKEGYGTPAYIKAQQALSAELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 471

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I++LQQKLI+LQ+ +V+
Sbjct: 472  KCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVMARNIPPIQDLQQKLIDLQSRVVV 531

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 532  PLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 591

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 592  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 651

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 652  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIE 711

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 712  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 771

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 772  ALRKLKHPSRSDKLRSFID 790



 Score =  728 bits (1878), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/624 (58%), Positives = 473/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E+++  R++ K LIKLGK RGYLT  EIND L
Sbjct: 154 KPLRMKISKAKERALMKEFGLDETVLSEEDMQKRRQRLKALIKLGKTRGYLTHVEINDHL 213

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+ ++D E +E++I T   + ++V E   D E L++++      ++++ EEA EAALSTV
Sbjct: 214 PDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTV 273

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 274 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNM 333

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 334 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 393

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +YIKA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 394 QALERFDKLRELFEKVHKVYDKEGYGTPAYIKAQQALSAELMTIRFTAKTIEKLCDMVRG 453

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 454 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSAVMARNIP 513

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I++LQQKLI+LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 514 PIQDLQQKLIDLQSRVVVPLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 573

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 574 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 633

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 634 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 693

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 694 DSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEE 753

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 754 VGKQFDVTRERIRQIEAKALRKLK 777


>gi|397661889|ref|YP_006502589.1| RNA polymerase sigma factor 70 [Taylorella equigenitalis ATCC 35865]
 gi|394350068|gb|AFN35982.1| RNA polymerase sigma factor 70 [Taylorella equigenitalis ATCC 35865]
          Length = 902

 Score =  737 bits (1903), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/622 (60%), Positives = 475/622 (76%), Gaps = 8/622 (1%)

Query: 811  KNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 869
            K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES++
Sbjct: 283  KGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMV 342

Query: 870  KTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
             T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++MYM
Sbjct: 343  STLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYM 402

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+EIV
Sbjct: 403  REMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIV 462

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
            DGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   FDK
Sbjct: 463  DGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAFDK 518

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK +L +
Sbjct: 519  MKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMLSV 578

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+ +
Sbjct: 579  CVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLEKE 638

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
            ++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 639  VILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 698

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQI
Sbjct: 699  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQI 758

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+
Sbjct: 759  LQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLS 818

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQI
Sbjct: 819  PEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQI 878

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR  KLK FLE
Sbjct: 879  EAKALRKLRHPSRADKLKSFLE 900



 Score =  717 bits (1852), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/617 (60%), Positives = 468/617 (75%), Gaps = 9/617 (1%)

Query: 21  KNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 79
           K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES++
Sbjct: 283 KGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMV 342

Query: 80  KTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 136
            T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++MYM
Sbjct: 343 STLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYM 402

Query: 137 REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
           REMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+EIV
Sbjct: 403 REMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIV 462

Query: 197 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
           DGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   FDK
Sbjct: 463 DGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAFDK 518

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK +L +
Sbjct: 519 MKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMLSV 578

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+ +
Sbjct: 579 CVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLEKE 638

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
           ++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 639 VILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 698

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQI
Sbjct: 699 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQI 758

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+
Sbjct: 759 LQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLS 818

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQI
Sbjct: 819 PEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQI 878

Query: 617 EAKALRKLR-PLAHDWL 632
           EAKALRKLR P   D L
Sbjct: 879 EAKALRKLRHPSRADKL 895


>gi|395009046|ref|ZP_10392619.1| RNA polymerase sigma factor, sigma-70 family [Acidovorax sp. CF316]
 gi|394312912|gb|EJE50015.1| RNA polymerase sigma factor, sigma-70 family [Acidovorax sp. CF316]
          Length = 792

 Score =  737 bits (1902), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/619 (58%), Positives = 468/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E++I T  
Sbjct: 172  FGLDETVLSEEDLAKRRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLN 231

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++       EE  E A    LSTVDS+FGRT DP++MYMREM
Sbjct: 232  DLGVAVYEQTPDAEALIITDNAPTGASEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 291

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 292  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVDGF 351

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 352  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRDLFEKVHK 411

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA + +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 412  IYDKEGYGTPAYVKAQHALSEELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 471

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP ++ELQQ+L++LQ  +V+
Sbjct: 472  KCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSTVMARNIPPVQELQQRLMDLQARVVV 531

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 532  PLTELKDINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 591

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 592  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 651

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PEEKIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP D
Sbjct: 652  FGFEPDASILAAKMEIPEEKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPID 711

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 712  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 771

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 772  ALRKLKHPSRSDKLRSFID 790



 Score =  727 bits (1876), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/624 (58%), Positives = 466/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D L
Sbjct: 154 KPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLIKLGKTRGYLTHVEISDHL 213

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E++I T   + ++V E   D E L++++       EE  E A    LSTV
Sbjct: 214 PDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPTGASEEEAEEAAEAALSTV 273

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 274 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNM 333

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 334 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 393

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +Y+KA + +S E++ IRFTAK+IEKLCD +R 
Sbjct: 394 QALERFDKLRDLFEKVHKIYDKEGYGTPAYVKAQHALSEELMTIRFTAKTIEKLCDMVRG 453

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 454 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSTVMARNIP 513

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ+L++LQ  +V+PL +L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 514 PVQELQQRLMDLQARVVVPLTELKDINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 573

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 574 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 633

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PEEKIRKIMKIAKEP+SME+P+GDD+
Sbjct: 634 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEEKIRKIMKIAKEPISMETPIGDDD 693

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 694 DSHLGDFIEDGANTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEE 753

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 754 VGKQFDVTRERIRQIEAKALRKLK 777


>gi|330826139|ref|YP_004389442.1| RNA polymerase sigma-710 subunit RpoD [Alicycliphilus denitrificans
            K601]
 gi|329311511|gb|AEB85926.1| RNA polymerase, sigma 70 subunit, RpoD [Alicycliphilus denitrificans
            K601]
          Length = 802

 Score =  735 bits (1898), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/619 (59%), Positives = 468/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 182  FGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLG 241

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+    T+ ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 242  DMGVAVYEQTPDAETLFQNNVAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 301

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ I  +VDG 
Sbjct: 302  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVDGF 361

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             +   + +    +     +EE        +   T  LEKLK E+L +F  +   F+KM K
Sbjct: 362  SNPEEADDYVAEEDFDEYDEEDDDDGKGGSKAMTRLLEKLKTEALDRFDELRSLFEKMHK 421

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY S +Y+K  + IS +++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 422  IYDKEGYGSPAYMKVQHEISAKLMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVD 481

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQQ LI+LQ+ +V+
Sbjct: 482  KCGMPQETFIKEFPPNLLNLQWVEKQAAAGKPWSAVMQRNIPPIQELQQHLIDLQSRVVV 541

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 542  PLAELKAINKRMNQGEANSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 601

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 602  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 661

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 662  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPID 721

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 722  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 781

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 782  ALRKLKHPSRSDKLRSFID 800



 Score =  725 bits (1872), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/621 (59%), Positives = 465/621 (74%), Gaps = 4/621 (0%)

Query: 9   KIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPED 68
           ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ 
Sbjct: 167 RMKISKAKERALMKEFGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDK 226

Query: 69  IIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSD 124
           ++D E +E ++     M ++V E   D ETL  +N+    T+ ++ EE  EAALSTVDS+
Sbjct: 227 LVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNNVAPTATTVEEAEEEAEAALSTVDSE 286

Query: 125 FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADK 184
           FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++
Sbjct: 287 FGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEE 346

Query: 185 ISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL 244
           I + ++ I  +VDG  +   + +    +     +EE        +   T  LEKLK E+L
Sbjct: 347 IREGKVVISTVVDGFSNPEEADDYVAEEDFDEYDEEDDDDGKGGSKAMTRLLEKLKTEAL 406

Query: 245 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 304
            +F  +   F+KM K ++KEGY S +Y+K  + IS +++ IRFTAK+IEKLCD +R Q++
Sbjct: 407 DRFDELRSLFEKMHKIYDKEGYGSPAYMKVQHEISAKLMTIRFTAKTIEKLCDMVRAQVD 466

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
            V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+
Sbjct: 467 DVRKKERELRRIIVDKCGMPQETFIKEFPPNLLNLQWVEKQAAAGKPWSAVMQRNIPPIQ 526

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           ELQQ LI+LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RG
Sbjct: 527 ELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSRDAKKEMIEANLRLVISIAKKYTNRG 586

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 587 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 646

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSH
Sbjct: 647 TINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSH 706

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGK
Sbjct: 707 LGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGK 766

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKALRKL+
Sbjct: 767 QFDVTRERIRQIEAKALRKLK 787


>gi|358636289|dbj|BAL23586.1| RNA polymerase sigma factor [Azoarcus sp. KH32C]
          Length = 663

 Score =  735 bits (1897), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/618 (59%), Positives = 468/618 (75%), Gaps = 19/618 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 43   KTRLKTLISLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIRVFDEAPAAEDL 102

Query: 890  MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++S+       E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 103  LMSDAVPSTVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 162

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+GL+ M+ AIS+CPTTI E+L   DK++ +E+++DE+VDGLID N ++        +
Sbjct: 163  RIEDGLRHMVQAISACPTTITEMLEIVDKVAGDEMRVDELVDGLIDPNAAAEEEAAALAE 222

Query: 1006 ---------------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                            +++++   E   A  +   L +LK ++L +F+ I    +   +A
Sbjct: 223  VDDEGAEDEEGGDDAGDDDDESSDEEKEAAANAASLAQLKADALARFAVIRKFNESKLEA 282

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
              K G    SY+     IS+E+L IRFTAK+IE+LCDT+R+ + QV   E+QIL++ V++
Sbjct: 283  LAKNGSQDLSYLALQQQISDELLNIRFTAKAIERLCDTVRHMVEQVRSHERQILQLCVDR 342

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             GMPR HFIKVFP  E++LNW+ +E  +   Y   L R  P++ E QQKLI+LQ+ I + 
Sbjct: 343  AGMPRQHFIKVFPGREVDLNWLKDEIGVGKSYAEGLMRVHPAVLEEQQKLIDLQSRIGIS 402

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L +L+D+NR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 403  LKELKDVNRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 462

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 463  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 522

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EPDP+ +A KM+MPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+  LAP+DA
Sbjct: 523  GQEPDPATLAEKMDMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLAPADA 582

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A+ +S+R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 583  AMYSSLREATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 642

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR  +L+ FL+
Sbjct: 643  LRKLRHPSRSERLRSFLD 660



 Score =  719 bits (1855), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/605 (59%), Positives = 458/605 (75%), Gaps = 19/605 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI LGKERGYLT++EI+D LP+D+ D E IE II TF  M I V +     E L
Sbjct: 43  KTRLKTLISLGKERGYLTYAEISDHLPDDVADAEQIEGIIATFNNMGIRVFDEAPAAEDL 102

Query: 100 MLSNITSDDDVEEATEA----ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++S+       E+  E     ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 103 LMSDAVPSTVDEDVAEEEAEQALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAK 162

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+GL+ M+ AIS+CPTTI E+L   DK++ +E+++DE+VDGLID N ++        +
Sbjct: 163 RIEDGLRHMVQAISACPTTITEMLEIVDKVAGDEMRVDELVDGLIDPNAAAEEEAAALAE 222

Query: 216 ---------------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
                           +++++   E   A  +   L +LK ++L +F+ I    +   +A
Sbjct: 223 VDDEGAEDEEGGDDAGDDDDESSDEEKEAAANAASLAQLKADALARFAVIRKFNESKLEA 282

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
             K G    SY+     IS+E+L IRFTAK+IE+LCDT+R+ + QV   E+QIL++ V++
Sbjct: 283 LAKNGSQDLSYLALQQQISDELLNIRFTAKAIERLCDTVRHMVEQVRSHERQILQLCVDR 342

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            GMPR HFIKVFP  E++LNW+ +E  +   Y   L R  P++ E QQKLI+LQ+ I + 
Sbjct: 343 AGMPRQHFIKVFPGREVDLNWLKDEIGVGKSYAEGLMRVHPAVLEEQQKLIDLQSRIGIS 402

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L +L+D+NR+M  GE K R+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 403 LKELKDVNRQMSTGEAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 462

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQET
Sbjct: 463 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQET 522

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EPDP+ +A KM+MPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+  LAP+DA
Sbjct: 523 GQEPDPATLAEKMDMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLAPADA 582

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A+ +S+R    ++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 583 AMYSSLREATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 642

Query: 621 LRKLR 625
           LRKLR
Sbjct: 643 LRKLR 647


>gi|319779662|ref|YP_004130575.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
 gi|317109686|gb|ADU92432.1| RNA polymerase sigma factor RpoD [Taylorella equigenitalis MCE9]
          Length = 840

 Score =  733 bits (1893), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/624 (60%), Positives = 476/624 (76%), Gaps = 8/624 (1%)

Query: 809  SKKNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIES 867
            + K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES
Sbjct: 219  TSKGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMES 278

Query: 868  IIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKM 924
            ++ T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++M
Sbjct: 279  MVSTLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRM 338

Query: 925  YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 984
            YMREMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+E
Sbjct: 339  YMREMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEE 398

Query: 985  IVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHF 1044
            IVDGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   F
Sbjct: 399  IVDGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAF 454

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            DKM+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK ++
Sbjct: 455  DKMKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMI 514

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
             + V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+
Sbjct: 515  SVCVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLE 574

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 575  KEVILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEG 634

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+R
Sbjct: 635  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITR 694

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            QILQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + 
Sbjct: 695  QILQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTST 754

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
            L+P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIR
Sbjct: 755  LSPEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIR 814

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR  KLK FLE
Sbjct: 815  QIEAKALRKLRHPSRADKLKSFLE 838



 Score =  714 bits (1842), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/617 (59%), Positives = 468/617 (75%), Gaps = 9/617 (1%)

Query: 21  KNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 79
           K + SF  K+ S++   E  R+  + LIK GK+ GYLT++EIND L +DI+D E +ES++
Sbjct: 221 KGSKSFRSKAESKKISDEERRQLVRSLIKQGKDHGYLTYAEINDVLSDDIVDSEAMESMV 280

Query: 80  KTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 136
            T   M I V E   + E L+L   SN+  DDDV++  E AL+TVDS+FGRT DP++MYM
Sbjct: 281 STLESMGIPVYEEAPNAEDLILAEPSNVNDDDDVDDEAEVALTTVDSEFGRTTDPVRMYM 340

Query: 137 REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
           REMGSVELL R  EIEIAKRIEEGLK M+ AI++ PTTI EIL    K+   + +I+EIV
Sbjct: 341 REMGSVELLNRTKEIEIAKRIEEGLKHMVMAIANSPTTINEILEHIQKVRDGKAQIEEIV 400

Query: 197 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
           DGLI    S +     G+   + ++   E+ +  +S+ Q+EKL+ ESL KF  +   FDK
Sbjct: 401 DGLI----SDDGEEYAGSGAADADEESEEAQTGGMSSLQIEKLREESLAKFDRVQKAFDK 456

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M+  +EK  + S++Y KA+  I +E+ G+RFTAK +EKL + LR QI +V ++EK ++ +
Sbjct: 457 MKAEYEKGRFQSQAYNKANQQIHDEISGVRFTAKMVEKLAEILRKQIERVRELEKAMISV 516

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V+K GMPR HFI  FP NE NL WV++E K +  Y   L R+IP I E+QQK I+L+ +
Sbjct: 517 CVDKVGMPREHFIDSFPGNETNLEWVNDELKKKPKYAEKLERSIPDIHEIQQKFIDLEKE 576

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
           ++LP+ +L+D+N++M+ GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 577 VILPIKELKDVNKRMVNGEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 636

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQI
Sbjct: 637 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQI 696

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQETG EPD +++A KM+MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+
Sbjct: 697 LQETGVEPDSAMLAEKMDMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLS 756

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P +AAL  SM  V  +++NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQI
Sbjct: 757 PEEAALQRSMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQI 816

Query: 617 EAKALRKLR-PLAHDWL 632
           EAKALRKLR P   D L
Sbjct: 817 EAKALRKLRHPSRADKL 833


>gi|114330327|ref|YP_746549.1| RNA polymerase sigma factor RpoD [Nitrosomonas eutropha C91]
 gi|114307341|gb|ABI58584.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas eutropha C91]
          Length = 749

 Score =  733 bits (1893), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/620 (59%), Positives = 469/620 (75%), Gaps = 23/620 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            +++E  R + K LI  GKERGYLT+SEIND LP+D++D + IESII     M ISV +  
Sbjct: 134  DDVELRRMRLKKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGISVHDEA 193

Query: 884  LDTETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
             D E L++S+     +D+DV E TEAALS+VDS+FGRT DP++MYMREMGSV LLTR+ E
Sbjct: 194  PDAEALLMSDTATAVADEDVAEETEAALSSVDSEFGRTTDPVRMYMREMGSVGLLTRESE 253

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            IEIAKRIE+GL+ MI AIS+CPT I  IL  A  +   +++ DE+VDG +D +  +   +
Sbjct: 254  IEIAKRIEDGLRHMIQAISACPTIIENILGLAADVESGQLRADELVDGFLDDD--TEEII 311

Query: 1001 IKG----------NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
             KG          + +  EE+  I S++AD+      K+K E L +F+ I   +D M+K 
Sbjct: 312  GKGMPEESLDQDFDSDETEEE-QIASANADML-----KMKNEVLERFAMIRQTYDDMKKI 365

Query: 1051 FEKEGYNSES--YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
             +K+G   +   Y +    IS E++ +RF+AK +E+LCDT R  +N +   E++I E+ V
Sbjct: 366  IDKKGGGRQDKKYKQLQEKISAELMAMRFSAKMVERLCDTQRAIVNDIRSCERKIAELCV 425

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
             +  MPR HFIK FP NE N++W+++E      Y+  L    P++ E QQK++ LQ    
Sbjct: 426  VRAKMPRNHFIKAFPGNETNIDWINSEVDANQPYSQSLEHYRPAVMEQQQKMLTLQEQAG 485

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            +P+ +L++INR+M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 486  IPIKELKEINRRMTTGEAKARSAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 545

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 546  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 605

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG EP+P+V+A KMEM EEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED + + P+
Sbjct: 606  ETGQEPEPAVLAEKMEMTEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVSTMEPA 665

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA+ A +R+V KD+L+SLTPRE+KVLRMRFGIEM++DHTLEEVG+QFDVTRERIRQIEA
Sbjct: 666  DAAIYAGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEA 725

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHP+R  +L+ FL+
Sbjct: 726  KALRKLRHPARSDRLRSFLD 745



 Score =  719 bits (1855), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/615 (59%), Positives = 462/615 (75%), Gaps = 24/615 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           +++E  R + K LI  GKERGYLT+SEIND LP+D++D + IESII     M ISV +  
Sbjct: 134 DDVELRRMRLKKLIMQGKERGYLTYSEINDHLPDDMLDADQIESIISMINDMGISVHDEA 193

Query: 94  LDTETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
            D E L++S+     +D+DV E TEAALS+VDS+FGRT DP++MYMREMGSV LLTR+ E
Sbjct: 194 PDAEALLMSDTATAVADEDVAEETEAALSSVDSEFGRTTDPVRMYMREMGSVGLLTRESE 253

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           IEIAKRIE+GL+ MI AIS+CPT I  IL  A  +   +++ DE+VDG +D +  +   +
Sbjct: 254 IEIAKRIEDGLRHMIQAISACPTIIENILGLAADVESGQLRADELVDGFLDDD--TEEII 311

Query: 211 IKG----------NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
            KG          + +  EE+  I S++AD+      K+K E L +F+ I   +D M+K 
Sbjct: 312 GKGMPEESLDQDFDSDETEEE-QIASANADML-----KMKNEVLERFAMIRQTYDDMKKI 365

Query: 261 FEKEGYNSES--YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
            +K+G   +   Y +    IS E++ +RF+AK +E+LCDT R  +N +   E++I E+ V
Sbjct: 366 IDKKGGGRQDKKYKQLQEKISAELMAMRFSAKMVERLCDTQRAIVNDIRSCERKIAELCV 425

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
            +  MPR HFIK FP NE N++W+++E      Y+  L    P++ E QQK++ LQ    
Sbjct: 426 VRAKMPRNHFIKAFPGNETNIDWINSEVDANQPYSQSLEHYRPAVMEQQQKMLTLQEQAG 485

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           +P+ +L++INR+M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 486 IPIKELKEINRRMTTGEAKARSAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 545

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 546 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 605

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG EP+P+V+A KMEM EEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED + + P+
Sbjct: 606 ETGQEPEPAVLAEKMEMTEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVSTMEPA 665

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA+ A +R+V KD+L+SLTPRE+KVLRMRFGIEM++DHTLEEVG+QFDVTRERIRQIEA
Sbjct: 666 DAAIYAGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEA 725

Query: 619 KALRKLR-PLAHDWL 632
           KALRKLR P   D L
Sbjct: 726 KALRKLRHPARSDRL 740


>gi|241764884|ref|ZP_04762887.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
 gi|241365587|gb|EER60323.1| RNA polymerase, sigma 70 subunit, RpoD [Acidovorax delafieldii 2AN]
          Length = 788

 Score =  733 bits (1892), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/619 (58%), Positives = 466/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E++I T  
Sbjct: 168  FGLDETVLSEEDLAKRRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLN 227

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++       EE  E A    LSTVDS+FGRT DP++MYMREM
Sbjct: 228  DLGVAVYEQTPDAEALIITDNAPSGATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 287

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 288  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVDGF 347

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 348  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRELFEKVHK 407

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 408  VYDKEGYGTPAYVKAQTALSEELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 467

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I++LQQKL +LQ+ +V+
Sbjct: 468  KCGMPQETFIKDFPPNLLNLKWVEKQAAAGKPWSAVMARNIPPIQDLQQKLADLQSRVVV 527

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 528  PLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 587

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 588  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 647

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 648  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIE 707

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 708  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 767

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 768  ALRKLKHPSRSDKLRSFID 786



 Score =  723 bits (1866), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/624 (58%), Positives = 464/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D L
Sbjct: 150 KPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLIKLGKTRGYLTHVEISDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E++I T   + ++V E   D E L++++       EE  E A    LSTV
Sbjct: 210 PDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPSGATEEEAEEAAEAALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 330 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 389

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 390 QALERFDKLRELFEKVHKVYDKEGYGTPAYVKAQTALSEELMTIRFTAKTIEKLCDMVRG 449

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 450 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLKWVEKQAAAGKPWSAVMARNIP 509

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I++LQQKL +LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 510 PIQDLQQKLADLQSRVVVPLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 569

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 570 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 629

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 630 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 689

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 690 DSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEE 749

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 750 VGKQFDVTRERIRQIEAKALRKLK 773


>gi|319762043|ref|YP_004125980.1| RNA polymerase sigma factor rpod [Alicycliphilus denitrificans BC]
 gi|317116604|gb|ADU99092.1| RNA polymerase sigma factor RpoD [Alicycliphilus denitrificans BC]
          Length = 802

 Score =  733 bits (1891), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/619 (59%), Positives = 467/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 182  FGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDKLVDAETMEVVVAMLG 241

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL  +N+    T+ ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 242  DMGVAVYEQTPDAETLFQNNVAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 301

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ I  +VDG 
Sbjct: 302  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEEIREGKVVISTVVDGF 361

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             +   + +    +     +EE        +   T  LEKLK E+L +F  +   F+KM K
Sbjct: 362  SNPEEADDYVAEEDFDEYDEEDDDDGKGGSKAMTRLLEKLKTEALDRFDELRSLFEKMHK 421

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY S +Y+K  + IS +++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 422  IYDKEGYGSPAYMKVQHEISAKLMTIRFTAKTIEKLCDMVRAQVDDVRKKERELRRIIVD 481

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  F K FP N +NL WV+ +      ++ ++ RNIP I+ELQQ LI+LQ+ +V+
Sbjct: 482  KCGMPQETFSKEFPSNLLNLQWVEKQAAAGKPWSAVMQRNIPPIQELQQHLIDLQSRVVV 541

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 542  PLAELKAINKRMNQGEANSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 601

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 602  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 661

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N  AP D
Sbjct: 662  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNTAPID 721

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 722  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 781

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 782  ALRKLKHPSRSDKLRSFID 800



 Score =  723 bits (1865), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/621 (59%), Positives = 464/621 (74%), Gaps = 4/621 (0%)

Query: 9   KIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPED 68
           ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ 
Sbjct: 167 RMKISKAKERALMKEFGLDETVLSEEDMAKRRSQLKKLITLGKTRGYLTQVEISDHLPDK 226

Query: 69  IIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSD 124
           ++D E +E ++     M ++V E   D ETL  +N+    T+ ++ EE  EAALSTVDS+
Sbjct: 227 LVDAETMEVVVAMLGDMGVAVYEQTPDAETLFQNNVAPTATTVEEAEEEAEAALSTVDSE 286

Query: 125 FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADK 184
           FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++
Sbjct: 287 FGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILNMGEE 346

Query: 185 ISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL 244
           I + ++ I  +VDG  +   + +    +     +EE        +   T  LEKLK E+L
Sbjct: 347 IREGKVVISTVVDGFSNPEEADDYVAEEDFDEYDEEDDDDGKGGSKAMTRLLEKLKTEAL 406

Query: 245 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 304
            +F  +   F+KM K ++KEGY S +Y+K  + IS +++ IRFTAK+IEKLCD +R Q++
Sbjct: 407 DRFDELRSLFEKMHKIYDKEGYGSPAYMKVQHEISAKLMTIRFTAKTIEKLCDMVRAQVD 466

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
            V + E+++  I+V+KCGMP+  F K FP N +NL WV+ +      ++ ++ RNIP I+
Sbjct: 467 DVRKKERELRRIIVDKCGMPQETFSKEFPSNLLNLQWVEKQAAAGKPWSAVMQRNIPPIQ 526

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           ELQQ LI+LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RG
Sbjct: 527 ELQQHLIDLQSRVVVPLAELKAINKRMNQGEANSRDAKKEMIEANLRLVISIAKKYTNRG 586

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 587 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 646

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSH
Sbjct: 647 TINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSH 706

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED N  AP DAA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEMS+DHTLEEVGK
Sbjct: 707 LGDFIEDSNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGK 766

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKALRKL+
Sbjct: 767 QFDVTRERIRQIEAKALRKLK 787


>gi|325983602|ref|YP_004296004.1| RNA polymerase sigma-70 subunit RpoD [Nitrosomonas sp. AL212]
 gi|325533121|gb|ADZ27842.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. AL212]
          Length = 740

 Score =  732 bits (1889), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/638 (60%), Positives = 481/638 (75%), Gaps = 24/638 (3%)

Query: 810  KKNAFSFDIKSNSR-EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 868
            K N+ S    SNS+ ++IE  R + KILI LGKERGYLT++EIND LP+D++D E IE I
Sbjct: 104  KINSASIIQSSNSQPQDIEARRMRLKILIGLGKERGYLTYAEINDHLPDDMLDAEQIEGI 163

Query: 869  IKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMY 925
            I     M ISV +   D ETL++S+  +    E+  E A   LSTVDS+FGRT DP++MY
Sbjct: 164  ISMINDMGISVHDEAPDVETLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMY 223

Query: 926  MREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEI 985
            MREMGSV LLTR+ EIEIAKRIE GL+ MI AIS+CP  I +I+  A ++ K  ++IDE+
Sbjct: 224  MREMGSVGLLTRESEIEIAKRIEGGLRHMIQAISACPPIIAKIIDLAVEVEKETMRIDEV 283

Query: 986  VDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLS---------------TEQLEKLK 1030
            VDGL+D N      +I  N+  +EE I  E SS DL+               +  L KLK
Sbjct: 284  VDGLLDANAQD---II--NEELSEEAIEQELSSNDLAGDEDEDEDSDGAAIASADLLKLK 338

Query: 1031 YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
             ++L +F+ I    ++M+   E +G   + YI+  + IS+E++ IRF+AK +EKLCDT R
Sbjct: 339  ADALERFAVIRQMHNEMQALLESDGPYHQGYIELQDKISSELMAIRFSAKMMEKLCDTQR 398

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
              +  V   E++I+++ V+K  MPR HFIK FP NE NL+W+  E K+   Y+  L    
Sbjct: 399  ELVGDVRNYERKIMDLCVSKAKMPRNHFIKTFPGNETNLDWIAQEIKVGKPYSQALEHYK 458

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
            P+I E Q  L+ L++ I +P+ DL++INRKM  GE KAR+AKREMTEANLRLVISIAKKY
Sbjct: 459  PAILEEQHNLLALRSKIGIPIKDLKEINRKMSTGEAKARRAKREMTEANLRLVISIAKKY 518

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 519  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 578

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK++RISRQILQETG EP+P+V+A KMEMPEEKIRKI+KI+KEP+SME+P+GDD
Sbjct: 579  HMIETINKMNRISRQILQETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDD 638

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            EDSHLGDFIED   +AP+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLE
Sbjct: 639  EDSHLGDFIEDAATMAPADAAVYASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLE 698

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EVGKQFDVTRERIRQIEAKALRKLRHP+R  +L+ FL+
Sbjct: 699  EVGKQFDVTRERIRQIEAKALRKLRHPARSERLRSFLD 736



 Score =  716 bits (1849), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/623 (60%), Positives = 470/623 (75%), Gaps = 24/623 (3%)

Query: 22  NAFSFDIKSNSR-EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 80
           N+ S    SNS+ ++IE  R + KILI LGKERGYLT++EIND LP+D++D E IE II 
Sbjct: 106 NSASIIQSSNSQPQDIEARRMRLKILIGLGKERGYLTYAEINDHLPDDMLDAEQIEGIIS 165

Query: 81  TFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMR 137
               M ISV +   D ETL++S+  +    E+  E A   LSTVDS+FGRT DP++MYMR
Sbjct: 166 MINDMGISVHDEAPDVETLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMYMR 225

Query: 138 EMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD 197
           EMGSV LLTR+ EIEIAKRIE GL+ MI AIS+CP  I +I+  A ++ K  ++IDE+VD
Sbjct: 226 EMGSVGLLTRESEIEIAKRIEGGLRHMIQAISACPPIIAKIIDLAVEVEKETMRIDEVVD 285

Query: 198 GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLS---------------TEQLEKLKYE 242
           GL+D N      +I  N+  +EE I  E SS DL+               +  L KLK +
Sbjct: 286 GLLDANAQD---II--NEELSEEAIEQELSSNDLAGDEDEDEDSDGAAIASADLLKLKAD 340

Query: 243 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 302
           +L +F+ I    ++M+   E +G   + YI+  + IS+E++ IRF+AK +EKLCDT R  
Sbjct: 341 ALERFAVIRQMHNEMQALLESDGPYHQGYIELQDKISSELMAIRFSAKMMEKLCDTQREL 400

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           +  V   E++I+++ V+K  MPR HFIK FP NE NL+W+  E K+   Y+  L    P+
Sbjct: 401 VGDVRNYERKIMDLCVSKAKMPRNHFIKTFPGNETNLDWIAQEIKVGKPYSQALEHYKPA 460

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E Q  L+ L++ I +P+ DL++INRKM  GE KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 461 ILEEQHNLLALRSKIGIPIKDLKEINRKMSTGEAKARRAKREMTEANLRLVISIAKKYTN 520

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 521 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 580

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQILQETG EP+P+V+A KMEMPEEKIRKI+KI+KEP+SME+P+GDDED
Sbjct: 581 IETINKMNRISRQILQETGQEPEPAVLAQKMEMPEEKIRKILKISKEPISMETPIGDDED 640

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED   +AP+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEV
Sbjct: 641 SHLGDFIEDAATMAPADAAVYASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEV 700

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 701 GKQFDVTRERIRQIEAKALRKLR 723


>gi|347817673|ref|ZP_08871107.1| RpoD family RNA polymerase sigma factor [Verminephrobacter
            aporrectodeae subsp. tuberculatae At4]
          Length = 647

 Score =  730 bits (1885), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/619 (58%), Positives = 467/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E++I T  
Sbjct: 27   FGLDETVLSEEDLARRRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLN 86

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D ETL+++        EE  E A    LSTVDS+FGRT DP++MYMREM
Sbjct: 87   DLGVAVYEQTPDAETLIITENAPTGASEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 146

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI +IL   ++I   ++ I  IVDG 
Sbjct: 147  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIADILNMGEEIRAGKVVISTIVDGF 206

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 207  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRQLFEKVHK 266

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y++A   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 267  VYDKEGYGTSAYVRAQQALSAELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 326

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  F+K FP N +NL W++ +      ++ ++ RN+P ++ELQQKL++LQ+ +V+
Sbjct: 327  KCGMPQETFVKEFPPNLLNLQWIEKQAGAGKPWSTVMARNVPPVQELQQKLMDLQSRVVV 386

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 387  PLTELKDINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 446

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 447  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 506

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 507  FGFEPDASLLAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIE 566

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 567  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 626

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 627  ALRKLKHPSRSDKLRSFID 645



 Score =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/624 (57%), Positives = 465/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D L
Sbjct: 9   KPLRMKISKAKERALMKEFGLDETVLSEEDLARRRSRLKTLIKLGKTRGYLTHVEISDHL 68

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E++I T   + ++V E   D ETL+++        EE  E A    LSTV
Sbjct: 69  PDKLVDAETLEAVITTLNDLGVAVYEQTPDAETLIITENAPTGASEEEAEEAAEAALSTV 128

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI +IL  
Sbjct: 129 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIADILNM 188

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I   ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 189 GEEIRAGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 248

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +Y++A   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 249 QALERFDKLRQLFEKVHKVYDKEGYGTSAYVRAQQALSAELMTIRFTAKTIEKLCDMVRG 308

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  F+K FP N +NL W++ +      ++ ++ RN+P
Sbjct: 309 QVDDVRKKERELRRIIVDKCGMPQETFVKEFPPNLLNLQWIEKQAGAGKPWSTVMARNVP 368

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQKL++LQ+ +V+PL +L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 369 PVQELQQKLMDLQSRVVVPLTELKDINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 428

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 429 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 488

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 489 MIETINKMNRISRQHLQEFGFEPDASLLAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 548

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 549 DSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEE 608

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 609 VGKQFDVTRERIRQIEAKALRKLK 632


>gi|365093304|ref|ZP_09330370.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. NO-1]
 gi|363414478|gb|EHL21627.1| RpoD family RNA polymerase sigma factor [Acidovorax sp. NO-1]
          Length = 776

 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/619 (59%), Positives = 472/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EIND LP+ ++D E +E++I T  
Sbjct: 156  FGLDETVLSEEDMAKRRARLKALIKLGKTRGYLTHVEINDHLPDKLVDAETLEAVITTLN 215

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++      ++++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 216  DLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 275

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I + ++ I  IVDG 
Sbjct: 276  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEIREGKVVISTIVDGF 335

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 336  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRELFEKVHK 395

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 396  VYDKEGYGTPNYQKAQKALSEELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 455

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ I+ RN+P I++LQQKLI+LQ+ +V+
Sbjct: 456  KCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSSIIARNVPPIQDLQQKLIDLQSRVVV 515

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 516  PLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 575

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 576  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 635

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 636  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIE 695

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 696  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 755

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 756  ALRKLKHPSRSDKLRSFID 774



 Score =  720 bits (1859), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/624 (58%), Positives = 470/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EIND L
Sbjct: 138 KPLRMKISKAKERALMKEFGLDETVLSEEDMAKRRARLKALIKLGKTRGYLTHVEINDHL 197

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+ ++D E +E++I T   + ++V E   D E L++++      ++++ EEA EAALSTV
Sbjct: 198 PDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTV 257

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 258 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNM 317

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            ++I + ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 318 GEEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 377

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +Y KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 378 QALERFDKLRELFEKVHKVYDKEGYGTPNYQKAQKALSEELMTIRFTAKTIEKLCDMVRG 437

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ I+ RN+P
Sbjct: 438 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAAGKPWSSIIARNVP 497

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I++LQQKLI+LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 498 PIQDLQQKLIDLQSRVVVPLAELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 557

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 558 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 617

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 618 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 677

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 678 DSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEE 737

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 738 VGKQFDVTRERIRQIEAKALRKLK 761


>gi|351731433|ref|ZP_08949124.1| RpoD family RNA polymerase sigma factor [Acidovorax radicis N35]
          Length = 741

 Score =  730 bits (1884), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/619 (59%), Positives = 472/619 (76%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EIND LP+ ++D E +E++I T  
Sbjct: 121  FGLDETVLSEEDMAKRRARLKALIKLGKTRGYLTHVEINDHLPDKLVDAETLEAVITTLN 180

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++      ++++ EEA EAALSTVDS+FGRT DP++MYMREM
Sbjct: 181  DLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 240

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   + I + ++ I  IVDG 
Sbjct: 241  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEDIREGKVVISTIVDGF 300

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+K+ K
Sbjct: 301  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRELFEKVHK 360

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 361  VYDKEGYGTPAYVKAQAALSAELMTIRFTAKTIEKLCDMVRGQVDDVRKKERELRRIIVD 420

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ I+ RNIP I++LQQKL++LQ+ +V+
Sbjct: 421  KCGMPQETFIKDFPPNLLNLQWVEKQANAGKPWSSIIARNIPPIQDLQQKLMDLQSRVVV 480

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 481  PLTELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 540

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 541  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 600

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 601  FGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPIE 660

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 661  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 720

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 721  ALRKLKHPSRSDKLRSFID 739



 Score =  720 bits (1859), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/624 (58%), Positives = 470/624 (75%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EIND L
Sbjct: 103 KPLRMKISKAKERALMKEFGLDETVLSEEDMAKRRARLKALIKLGKTRGYLTHVEINDHL 162

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P+ ++D E +E++I T   + ++V E   D E L++++      ++++ EEA EAALSTV
Sbjct: 163 PDKLVDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPAGATEEEAEEAAEAALSTV 222

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 223 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNM 282

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            + I + ++ I  IVDG  + N + +    +     +E         +   T++LE+LK 
Sbjct: 283 GEDIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKK 342

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  +   F+K+ K ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 343 QALERFDKLRELFEKVHKVYDKEGYGTPAYVKAQAALSAELMTIRFTAKTIEKLCDMVRG 402

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++ V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      ++ I+ RNIP
Sbjct: 403 QVDDVRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQANAGKPWSSIIARNIP 462

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I++LQQKL++LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 463 PIQDLQQKLMDLQSRVVVPLTELKGINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYT 522

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 523 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 582

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 583 MIETINKMNRISRQHLQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDD 642

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 643 DSHLGDFIEDGANTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEE 702

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 703 VGKQFDVTRERIRQIEAKALRKLK 726


>gi|291614899|ref|YP_003525056.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
            ES-1]
 gi|291585011|gb|ADE12669.1| RNA polymerase, sigma 70 subunit, RpoD [Sideroxydans lithotrophicus
            ES-1]
          Length = 654

 Score =  729 bits (1883), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/615 (60%), Positives = 466/615 (75%), Gaps = 9/615 (1%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            +EIE  R + K LI LGKERGYLTF+EIND LP D+++ E +E ++     M I+V +  
Sbjct: 40   QEIEARRTRLKALILLGKERGYLTFAEINDHLP-DMLEVEQVEGVVSMINDMGITVCDVA 98

Query: 884  LDTETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
             DTE+L+++        +D  E  EAA+STVDS+FGRT DP++MYMREMG V LLTR  E
Sbjct: 99   PDTESLVMNETAPPVADEDAAEEAEAAISTVDSEFGRTTDPVRMYMREMGVVNLLTRQDE 158

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS---- 996
            IEIAKRIE+GLK MI AIS+CP TI EIL  ADK++K E++IDE++DG ID    +    
Sbjct: 159  IEIAKRIEDGLKHMIQAISACPATIAEILALADKVAKEELRIDELIDGFIDTQDEAMVSE 218

Query: 997  -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
                     +   +E+   E      +   L +LK ++L++F+ IS  F K+ KA+EK G
Sbjct: 219  VAEEEETEEEEEEDEEEESEEDGEAAAAANLAQLKEDALVRFALISDLFTKLGKAYEKYG 278

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y S+ Y K    IS+E++  RF+AK ++ LC+T+R  + +V   E+ I E+ V K  MPR
Sbjct: 279  YRSKQYDKLQQQISDELMQFRFSAKQVDALCETMRGLVEEVRSCERSIQELCVTKAHMPR 338

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             HFIKVFP NE NL WV +E   +  Y+  L R   +I + Q+K++ LQ  + +P+ DL+
Sbjct: 339  THFIKVFPLNEGNLEWVKHEMASKKAYSETLSRYEAAIVDQQKKMLALQQRVGIPILDLK 398

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            +IN++M  GE KAR+AKR+M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 399  EINKQMTNGEAKARRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 458

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E D
Sbjct: 459  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGMEAD 518

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
             + +AIKMEMPE+KIRKI+KIAKEP+SME+PVGDD+DSHLGDFIED N LAP +AA+  S
Sbjct: 519  AATLAIKMEMPEDKIRKILKIAKEPISMETPVGDDDDSHLGDFIEDANSLAPIEAAVYDS 578

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +R+V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 579  LRNVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 638

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  KLK FL+G+
Sbjct: 639  HPSRSEKLKSFLDGE 653



 Score =  709 bits (1829), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/600 (60%), Positives = 454/600 (75%), Gaps = 9/600 (1%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           +EIE  R + K LI LGKERGYLTF+EIND LP D+++ E +E ++     M I+V +  
Sbjct: 40  QEIEARRTRLKALILLGKERGYLTFAEINDHLP-DMLEVEQVEGVVSMINDMGITVCDVA 98

Query: 94  LDTETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
            DTE+L+++        +D  E  EAA+STVDS+FGRT DP++MYMREMG V LLTR  E
Sbjct: 99  PDTESLVMNETAPPVADEDAAEEAEAAISTVDSEFGRTTDPVRMYMREMGVVNLLTRQDE 158

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS---- 206
           IEIAKRIE+GLK MI AIS+CP TI EIL  ADK++K E++IDE++DG ID    +    
Sbjct: 159 IEIAKRIEDGLKHMIQAISACPATIAEILALADKVAKEELRIDELIDGFIDTQDEAMVSE 218

Query: 207 -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
                    +   +E+   E      +   L +LK ++L++F+ IS  F K+ KA+EK G
Sbjct: 219 VAEEEETEEEEEEDEEEESEEDGEAAAAANLAQLKEDALVRFALISDLFTKLGKAYEKYG 278

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           Y S+ Y K    IS+E++  RF+AK ++ LC+T+R  + +V   E+ I E+ V K  MPR
Sbjct: 279 YRSKQYDKLQQQISDELMQFRFSAKQVDALCETMRGLVEEVRSCERSIQELCVTKAHMPR 338

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            HFIKVFP NE NL WV +E   +  Y+  L R   +I + Q+K++ LQ  + +P+ DL+
Sbjct: 339 THFIKVFPLNEGNLEWVKHEMASKKAYSETLSRYEAAIVDQQKKMLALQQRVGIPILDLK 398

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           +IN++M  GE KAR+AKR+M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 399 EINKQMTNGEAKARRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 458

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E D
Sbjct: 459 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGMEAD 518

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
            + +AIKMEMPE+KIRKI+KIAKEP+SME+PVGDD+DSHLGDFIED N LAP +AA+  S
Sbjct: 519 AATLAIKMEMPEDKIRKILKIAKEPISMETPVGDDDDSHLGDFIEDANSLAPIEAAVYDS 578

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +R+V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 579 LRNVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 638


>gi|339481775|ref|YP_004693561.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. Is79A3]
 gi|338803920|gb|AEJ00162.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosomonas sp. Is79A3]
          Length = 746

 Score =  729 bits (1883), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 381/626 (60%), Positives = 471/626 (75%), Gaps = 22/626 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++IE  R + K+LI LGKERGYLT++EIND LP+D++D E IE II     M ISV +  
Sbjct: 126  QDIEARRMRLKMLIGLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMINDMGISVHDEA 185

Query: 884  LDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
             D ETL++S+  +    E+  E A   LSTVDS+FGRT DP++MYMREMGSV LLTR+ E
Sbjct: 186  PDAETLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMYMREMGSVGLLTRESE 245

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            IEIAKRIE GL+ MI AIS+CP  I  I+  A ++ K+ I+IDE+VDGL+D N      +
Sbjct: 246  IEIAKRIEGGLRHMIQAISACPPIIARIVDLATEVEKDIIRIDEVVDGLLDANAQD---I 302

Query: 1001 IKGNKNNNEEKILIE--------------SSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
            I  N+  +EE +  E                SA +++  L KLK ++L +FS I   + +
Sbjct: 303  I--NEEFSEESLEQELAASDLGDEDEDEDGDSAAIASADLLKLKADALERFSVIREIYSE 360

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M+   EK G   + Y++  + IS+E++ IRF+AK +EKLCDT R  +  V   E++I+++
Sbjct: 361  MQNLLEKNGPYHQEYVELQDKISSELMAIRFSAKMVEKLCDTQRELVGDVRNYERKIMDL 420

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V+K  MPR HFIK FP NE NL WV  E +    Y+  L    PSI E QQ L+ L+  
Sbjct: 421  CVSKAKMPRNHFIKTFPGNETNLEWVKQEIEAGKPYSQALEHYRPSILEEQQNLLALKNK 480

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
            I +P+ DL++INRKM  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 481  IGIPIKDLKEINRKMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 540

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQI
Sbjct: 541  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 600

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG EP+P+++A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   +A
Sbjct: 601  LQETGQEPEPAILAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDAATMA 660

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQI
Sbjct: 661  PADAAVYASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 720

Query: 1407 EAKALRKLRHPSRYYKLKIFLEGKKN 1432
            EAKALRKLRHP+R  +L+ FL+   N
Sbjct: 721  EAKALRKLRHPARSERLRSFLDTGNN 746



 Score =  713 bits (1841), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/609 (61%), Positives = 460/609 (75%), Gaps = 22/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++IE  R + K+LI LGKERGYLT++EIND LP+D++D E IE II     M ISV +  
Sbjct: 126 QDIEARRMRLKMLIGLGKERGYLTYAEINDHLPDDMLDAEQIEGIISMINDMGISVHDEA 185

Query: 94  LDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
            D ETL++S+  +    E+  E A   LSTVDS+FGRT DP++MYMREMGSV LLTR+ E
Sbjct: 186 PDAETLLMSDAATTVADEDVAEEAEAALSTVDSEFGRTTDPVRMYMREMGSVGLLTRESE 245

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           IEIAKRIE GL+ MI AIS+CP  I  I+  A ++ K+ I+IDE+VDGL+D N      +
Sbjct: 246 IEIAKRIEGGLRHMIQAISACPPIIARIVDLATEVEKDIIRIDEVVDGLLDANAQD---I 302

Query: 211 IKGNKNNNEEKILIE--------------SSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
           I  N+  +EE +  E                SA +++  L KLK ++L +FS I   + +
Sbjct: 303 I--NEEFSEESLEQELAASDLGDEDEDEDGDSAAIASADLLKLKADALERFSVIREIYSE 360

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M+   EK G   + Y++  + IS+E++ IRF+AK +EKLCDT R  +  V   E++I+++
Sbjct: 361 MQNLLEKNGPYHQEYVELQDKISSELMAIRFSAKMVEKLCDTQRELVGDVRNYERKIMDL 420

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V+K  MPR HFIK FP NE NL WV  E +    Y+  L    PSI E QQ L+ L+  
Sbjct: 421 CVSKAKMPRNHFIKTFPGNETNLEWVKQEIEAGKPYSQALEHYRPSILEEQQNLLALKNK 480

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
           I +P+ DL++INRKM  GE KAR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 481 IGIPIKDLKEINRKMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNI 540

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQI
Sbjct: 541 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI 600

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQETG EP+P+++A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   +A
Sbjct: 601 LQETGQEPEPAILAQKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDAATMA 660

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P+DAA+ AS+R V KDIL+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQI
Sbjct: 661 PADAAVYASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQI 720

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 721 EAKALRKLR 729


>gi|121604510|ref|YP_981839.1| RpoD family RNA polymerase sigma factor [Polaromonas
            naphthalenivorans CJ2]
 gi|120593479|gb|ABM36918.1| RNA polymerase, sigma 70 subunit, RpoD [Polaromonas naphthalenivorans
            CJ2]
          Length = 736

 Score =  729 bits (1881), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/619 (59%), Positives = 466/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E+I   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E +I    
Sbjct: 116  FGLDETVLSEEDILKRRVRLKTLIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVINMLN 175

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N      ++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 176  DMGVAVYEQAPDAETLLLNNTGATVATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 235

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+  AD I + ++ I  +VDG 
Sbjct: 236  GTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRLADDIREGKVVISTVVDGF 295

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E+        +   T++LE+LK E+L +F  +  + +K++K
Sbjct: 296  SNPNEADDYVAEEDFDEFDEDDDDDGKGGSKALTKKLEELKKEALSRFEKVGEYAEKVKK 355

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             +EKEGY   +Y+K    +S+E++ +RFTAK+IEKLCD LR Q+  V + E+++  I+V 
Sbjct: 356  LYEKEGYGGPTYLKTQKALSDELMTVRFTAKTIEKLCDLLRGQVLDVRKKERELRRIIVE 415

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP I+ELQ KL  LQ  +V+
Sbjct: 416  KCGMPQEVFIKDFPPNLLNLKWVEKQVAAGKPWSNVMARNIPPIQELQTKLGELQARVVV 475

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 476  PLLHLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 535

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ LQE
Sbjct: 536  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRLSRQHLQE 595

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PEEKIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +
Sbjct: 596  FGFEPDASILAEKMEIPEEKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDGANTAPLE 655

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 656  AAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAK 715

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 716  ALRKLKHPSRSDKLRSFID 734



 Score =  719 bits (1856), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/624 (59%), Positives = 464/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E+I   R + K LIKLGK RGYLT  EI+D L
Sbjct: 98  KPLRMKISKAKERALMKEFGLDETVLSEEDILKRRVRLKTLIKLGKTRGYLTHGEISDHL 157

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N      ++++ EE  EAALSTV
Sbjct: 158 PDKLVDAETLEVVINMLNDMGVAVYEQAPDAETLLLNNTGATVATEEEAEEEAEAALSTV 217

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EI+  
Sbjct: 218 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMKMMEAISESPATIAEIMRL 277

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           AD I + ++ I  +VDG  + N + +    +     +E+        +   T++LE+LK 
Sbjct: 278 ADDIREGKVVISTVVDGFSNPNEADDYVAEEDFDEFDEDDDDDGKGGSKALTKKLEELKK 337

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +  + +K++K +EKEGY   +Y+K    +S+E++ +RFTAK+IEKLCD LR 
Sbjct: 338 EALSRFEKVGEYAEKVKKLYEKEGYGGPTYLKTQKALSDELMTVRFTAKTIEKLCDLLRG 397

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q+  V + E+++  I+V KCGMP+  FIK FP N +NL WV+ +      ++ ++ RNIP
Sbjct: 398 QVLDVRKKERELRRIIVEKCGMPQEVFIKDFPPNLLNLKWVEKQVAAGKPWSNVMARNIP 457

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I+ELQ KL  LQ  +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 458 PIQELQTKLGELQARVVVPLLHLKDINKRMNEGESNSRDAKKEMIEANLRLVISIAKKYT 517

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 518 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 577

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++R+SRQ LQE G EPD S++A KME+PEEKIRKIMKIAKEP+SME+P+GDD+
Sbjct: 578 MIETINKMNRLSRQHLQEFGFEPDASILAEKMEIPEEKIRKIMKIAKEPISMETPIGDDD 637

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 638 DSHLGDFIEDGANTAPLEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEE 697

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 698 VGKQFDVTRERIRQIEAKALRKLK 721


>gi|399116768|emb|CCG19577.1| RNA polymerase sigma factor 70 [Taylorella asinigenitalis 14/45]
          Length = 918

 Score =  728 bits (1880), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/605 (60%), Positives = 467/605 (77%), Gaps = 7/605 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R+  + LIK G+++GYLT++EIND L +DI+D E +ES++ T   M I V E   + 
Sbjct: 316  EERRQLIRSLIKQGRDQGYLTYAEINDVLSDDIVDTEQMESMVTTLGDMGIPVYEEAPNA 375

Query: 887  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            E L+L   SNI  DDDV++  E AL+TVDSDFGRT DP++MYMREMGS+ELL R  EIEI
Sbjct: 376  EDLILAEPSNINDDDDVDDEAEVALTTVDSDFGRTTDPVRMYMREMGSIELLNRSKEIEI 435

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IEEGLK M+ AI+S PTTI EIL    K+ + + +I+EIVDGL+    + +     G
Sbjct: 436  AKMIEEGLKHMVMAIASSPTTIHEILEHIQKVKEGKAQIEEIVDGLM----TDDGEEYAG 491

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  ++ +    E+ +  +S+ Q+EKL+ ESL KF  +   +DKM K +EK  + S +Y K
Sbjct: 492  SGASDADDDTEEAQTGGMSSGQIEKLREESLAKFDRVQKAYDKMMKEYEKGRFQSPAYNK 551

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A+  I +E+ G+RFTAK +EKL + LR QI +V  +EK +L++ V+K GMPR HFI  FP
Sbjct: 552  ANQEIHDEISGVRFTAKMVEKLAEKLRKQIERVRSLEKDMLKVCVDKVGMPREHFIDSFP 611

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+WV++E K +  Y   L R++P I E+QQK I+L+ +++LP+ +L+++N++M+ 
Sbjct: 612  GNETNLDWVNSELKKKPKYAEKLERSVPDIHEIQQKFIDLEKEVILPIKELKNVNKRMVN 671

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 672  GEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 731

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQILQETG EPD +++A KM
Sbjct: 732  STYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKM 791

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            +MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+P +AAL  SM  V  ++
Sbjct: 792  DMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMTEVFDEV 851

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            +NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQIEAKA+RKL+HPSR  KL
Sbjct: 852  INSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRADKL 911

Query: 1424 KIFLE 1428
            + FLE
Sbjct: 912  RSFLE 916



 Score =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/600 (60%), Positives = 460/600 (76%), Gaps = 8/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R+  + LIK G+++GYLT++EIND L +DI+D E +ES++ T   M I V E   + 
Sbjct: 316 EERRQLIRSLIKQGRDQGYLTYAEINDVLSDDIVDTEQMESMVTTLGDMGIPVYEEAPNA 375

Query: 97  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           E L+L   SNI  DDDV++  E AL+TVDSDFGRT DP++MYMREMGS+ELL R  EIEI
Sbjct: 376 EDLILAEPSNINDDDDVDDEAEVALTTVDSDFGRTTDPVRMYMREMGSIELLNRSKEIEI 435

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IEEGLK M+ AI+S PTTI EIL    K+ + + +I+EIVDGL+    + +     G
Sbjct: 436 AKMIEEGLKHMVMAIASSPTTIHEILEHIQKVKEGKAQIEEIVDGLM----TDDGEEYAG 491

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  ++ +    E+ +  +S+ Q+EKL+ ESL KF  +   +DKM K +EK  + S +Y K
Sbjct: 492 SGASDADDDTEEAQTGGMSSGQIEKLREESLAKFDRVQKAYDKMMKEYEKGRFQSPAYNK 551

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A+  I +E+ G+RFTAK +EKL + LR QI +V  +EK +L++ V+K GMPR HFI  FP
Sbjct: 552 ANQEIHDEISGVRFTAKMVEKLAEKLRKQIERVRSLEKDMLKVCVDKVGMPREHFIDSFP 611

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+WV++E K +  Y   L R++P I E+QQK I+L+ +++LP+ +L+++N++M+ 
Sbjct: 612 GNETNLDWVNSELKKKPKYAEKLERSVPDIHEIQQKFIDLEKEVILPIKELKNVNKRMVN 671

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 672 GEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 731

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQILQETG EPD +++A KM
Sbjct: 732 STYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKM 791

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           +MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+P +AAL  SM  V  ++
Sbjct: 792 DMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMTEVFDEV 851

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           +NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQIEAKA+RKL+ P   D L
Sbjct: 852 INSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRADKL 911


>gi|121609019|ref|YP_996826.1| RpoD family RNA polymerase sigma factor [Verminephrobacter eiseniae
            EF01-2]
 gi|121553659|gb|ABM57808.1| RNA polymerase, sigma 70 subunit, RpoD family [Verminephrobacter
            eiseniae EF01-2]
          Length = 635

 Score =  728 bits (1878), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/619 (58%), Positives = 468/619 (75%), Gaps = 4/619 (0%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ ++D E +E++I T  
Sbjct: 15   FGLDETVLSEEDLARRRSRLKTLIKLGKTRGYLTHVEISDHLPDKLVDAETLEAVITTLN 74

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             + ++V E   D E L++++       EE  E A    LSTVDS+FGRT DP++MYMREM
Sbjct: 75   DLGVAVYEQTPDAEALIITDNAPTGASEEEAEEAAEAALSTVDSEFGRTTDPVRMYMREM 134

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I   ++ I  IVDG 
Sbjct: 135  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEIRAGKVVISTIVDGF 194

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +E         +   T++LE+LK ++L +F  +   F+KM K
Sbjct: 195  SNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKLRDLFEKMHK 254

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++K+GY + +Y++A   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 255  VYDKDGYGTLAYVQAQQALSAELMTIRFTAKTIEKLCDMVRGQVDDVRRKERELRRIIVD 314

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            KCGMP+  FIK FP N +NL WV+ +  +   ++ I+ RNIP I++LQQKL++LQ+ +V+
Sbjct: 315  KCGMPQETFIKDFPPNLLNLQWVEKQAAMGKPWSSIIARNIPPIQDLQQKLMDLQSRVVV 374

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 375  PLTELKVINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 434

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 435  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 494

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED +  AP +
Sbjct: 495  FGFEPDASLLAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDASNTAPIE 554

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 555  AAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAK 614

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKL+HPSR  KL+ F++
Sbjct: 615  ALRKLKHPSRSDKLRSFID 633



 Score =  717 bits (1850), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/620 (58%), Positives = 464/620 (74%), Gaps = 4/620 (0%)

Query: 10  IKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDI 69
           +K  K KE  L   F  D    S E++   R + K LIKLGK RGYLT  EI+D LP+ +
Sbjct: 1   MKISKAKERALMKEFGLDETVLSEEDLARRRSRLKTLIKLGKTRGYLTHVEISDHLPDKL 60

Query: 70  IDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDF 125
           +D E +E++I T   + ++V E   D E L++++       EE  E A    LSTVDS+F
Sbjct: 61  VDAETLEAVITTLNDLGVAVYEQTPDAEALIITDNAPTGASEEEAEEAAEAALSTVDSEF 120

Query: 126 GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 185
           GRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL   ++I
Sbjct: 121 GRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILNMGEEI 180

Query: 186 SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 245
              ++ I  IVDG  + N + +    +     +E         +   T++LE+LK ++L 
Sbjct: 181 RAGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALE 240

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           +F  +   F+KM K ++K+GY + +Y++A   +S E++ IRFTAK+IEKLCD +R Q++ 
Sbjct: 241 RFDKLRDLFEKMHKVYDKDGYGTLAYVQAQQALSAELMTIRFTAKTIEKLCDMVRGQVDD 300

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +  +   ++ I+ RNIP I++
Sbjct: 301 VRRKERELRRIIVDKCGMPQETFIKDFPPNLLNLQWVEKQAAMGKPWSSIIARNIPPIQD 360

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
           LQQKL++LQ+ +V+PL +L+ IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 361 LQQKLMDLQSRVVVPLTELKVINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGL 420

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 421 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 480

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHL
Sbjct: 481 INKMNRISRQHLQEFGFEPDASLLAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHL 540

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDFIED +  AP +AA+ A +R VVKDIL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQ
Sbjct: 541 GDFIEDASNTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQ 600

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKL+
Sbjct: 601 FDVTRERIRQIEAKALRKLK 620


>gi|348590104|ref|YP_004874566.1| RNA polymerase sigma factor RpoD [Taylorella asinigenitalis MCE3]
 gi|347974008|gb|AEP36543.1| RNA polymerase sigma factor RpoD [Taylorella asinigenitalis MCE3]
          Length = 865

 Score =  727 bits (1876), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/605 (60%), Positives = 468/605 (77%), Gaps = 7/605 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R+  + LIK G+++GYLT++EIND L +DI+D E +ES++ T   M I V E   + 
Sbjct: 263  EERRQLIRSLIKQGRDQGYLTYAEINDVLSDDIVDTEQMESMVTTLGDMGIPVYEEAPNA 322

Query: 887  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            E L+L   SNI  DDDV++  E AL+TVDSDFGRT DP++MYMREMGS+ELL R  EIEI
Sbjct: 323  EDLILAEPSNINDDDDVDDEAEVALTTVDSDFGRTTDPVRMYMREMGSIELLNRSKEIEI 382

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IEEGLK M+ AI+S PTTI EIL    K+ + + +I+EIVDGL+    + +     G
Sbjct: 383  AKMIEEGLKHMVMAIASSPTTIHEILEHIQKVKEGKAQIEEIVDGLM----TDDGEEYAG 438

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  ++ ++   E+ +  +S+ Q+EKL+ ESL KF  +   +DKM K +EK  + S +Y K
Sbjct: 439  SGASDADEDTEEAQTGGMSSGQIEKLREESLSKFDRVQKAYDKMMKEYEKGRFQSPAYNK 498

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A+  I +E+ G+RFTAK +EKL + LR QI +V  +EK +L++ V+K GMPR HFI  FP
Sbjct: 499  ANQEIHDEISGVRFTAKMVEKLAEKLRKQIERVRSLEKDMLKVCVDKVGMPREHFIDSFP 558

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+WV++E K +  Y   L R++P I E+QQK I+L+ +++LP+ +L+++N++M+ 
Sbjct: 559  GNETNLDWVNSELKKKPKYAEKLERSVPDIHEIQQKFIDLEKEVILPIKELKNVNKRMVN 618

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 619  GEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 678

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQILQETG EPD +++A KM
Sbjct: 679  STYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKM 738

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            +MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+P +AAL  SM  V  ++
Sbjct: 739  DMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMTEVFDEV 798

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            +NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQIEAKA+RKL+HPSR  KL
Sbjct: 799  INSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRADKL 858

Query: 1424 KIFLE 1428
            + FLE
Sbjct: 859  RSFLE 863



 Score =  708 bits (1827), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/600 (60%), Positives = 461/600 (76%), Gaps = 8/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R+  + LIK G+++GYLT++EIND L +DI+D E +ES++ T   M I V E   + 
Sbjct: 263 EERRQLIRSLIKQGRDQGYLTYAEINDVLSDDIVDTEQMESMVTTLGDMGIPVYEEAPNA 322

Query: 97  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           E L+L   SNI  DDDV++  E AL+TVDSDFGRT DP++MYMREMGS+ELL R  EIEI
Sbjct: 323 EDLILAEPSNINDDDDVDDEAEVALTTVDSDFGRTTDPVRMYMREMGSIELLNRSKEIEI 382

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IEEGLK M+ AI+S PTTI EIL    K+ + + +I+EIVDGL+    + +     G
Sbjct: 383 AKMIEEGLKHMVMAIASSPTTIHEILEHIQKVKEGKAQIEEIVDGLM----TDDGEEYAG 438

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  ++ ++   E+ +  +S+ Q+EKL+ ESL KF  +   +DKM K +EK  + S +Y K
Sbjct: 439 SGASDADEDTEEAQTGGMSSGQIEKLREESLSKFDRVQKAYDKMMKEYEKGRFQSPAYNK 498

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A+  I +E+ G+RFTAK +EKL + LR QI +V  +EK +L++ V+K GMPR HFI  FP
Sbjct: 499 ANQEIHDEISGVRFTAKMVEKLAEKLRKQIERVRSLEKDMLKVCVDKVGMPREHFIDSFP 558

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+WV++E K +  Y   L R++P I E+QQK I+L+ +++LP+ +L+++N++M+ 
Sbjct: 559 GNETNLDWVNSELKKKPKYAEKLERSVPDIHEIQQKFIDLEKEVILPIKELKNVNKRMVN 618

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KA+KAK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 619 GEAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 678

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQAR IRIPVHMIETINKI+RI+RQILQETG EPD +++A KM
Sbjct: 679 STYATWWIRQAITRSIADQARIIRIPVHMIETINKINRITRQILQETGVEPDSAMLAEKM 738

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           +MP EKIRKI+KI+K+P+SME+P+GDD+DSHLGDFIED + L+P +AAL  SM  V  ++
Sbjct: 739 DMPIEKIRKILKISKDPISMETPIGDDDDSHLGDFIEDTSTLSPEEAALQRSMTEVFDEV 798

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           +NSLT RE KVLRMRFGI MSSD TLEEVGKQFDVTRERIRQIEAKA+RKL+ P   D L
Sbjct: 799 INSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKAIRKLKHPSRADKL 858


>gi|398808666|ref|ZP_10567526.1| RNA polymerase sigma factor, sigma-70 family [Variovorax sp. CF313]
 gi|398087018|gb|EJL77616.1| RNA polymerase sigma factor, sigma-70 family [Variovorax sp. CF313]
          Length = 778

 Score =  726 bits (1875), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/629 (58%), Positives = 470/629 (74%), Gaps = 14/629 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 148  FGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLN 207

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N     T+ ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 208  DMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 267

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  A +I + ++ I  IVDG 
Sbjct: 268  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRLAAEIREGKVVISTIVDGF 327

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK E+L +F  I+  F+K+ K
Sbjct: 328  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKREALERFDRIAGMFEKVHK 387

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 388  IYDKEGYGTPAYVKAQEALSAELMTIRFTAKTIEKLCDLVRTQVDDVRKKERELRRIIVD 447

Query: 1110 KCGMPRLHFIKVF----------PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            KCG P+  FI+ F            N +NL WV+ +      ++ +L RNIP ++ELQQ+
Sbjct: 448  KCGFPQDEFIRDFSGYDKNGNRIASNLLNLKWVEKQAAAGKPWSAVLARNIPPVQELQQR 507

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L ++Q+ +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 508  LTDIQSRVVVPLTQLKDINKRMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLD 567

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 568  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 627

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 628  NRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 687

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVT
Sbjct: 688  EDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVT 747

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKL+HPSR  KL+ F++
Sbjct: 748  RERIRQIEAKALRKLKHPSRSDKLRSFID 776



 Score =  716 bits (1849), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/634 (57%), Positives = 468/634 (73%), Gaps = 14/634 (2%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 130 KPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHL 189

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL+L+N     T+ ++ EE  EAALSTV
Sbjct: 190 PDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTV 249

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 250 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRL 309

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A +I + ++ I  IVDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 310 AAEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKR 369

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  I+  F+K+ K ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 370 EALERFDRIAGMFEKVHKIYDKEGYGTPAYVKAQEALSAELMTIRFTAKTIEKLCDLVRT 429

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVF----------PENEINLNWVDNETKIQHD 351
           Q++ V + E+++  I+V+KCG P+  FI+ F            N +NL WV+ +      
Sbjct: 430 QVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGNRIASNLLNLKWVEKQAAAGKP 489

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           ++ +L RNIP ++ELQQ+L ++Q+ +V+PL  L+DIN++M  GE  +R AK+EM EANLR
Sbjct: 490 WSAVLARNIPPVQELQQRLTDIQSRVVVPLTQLKDINKRMNEGESSSRDAKKEMIEANLR 549

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 550 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 609

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+
Sbjct: 610 QARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPI 669

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGI
Sbjct: 670 SMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGI 729

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKL+
Sbjct: 730 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 763


>gi|319792617|ref|YP_004154257.1| RNA polymerase sigma-70 subunit RpoD [Variovorax paradoxus EPS]
 gi|315595080|gb|ADU36146.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus EPS]
          Length = 778

 Score =  726 bits (1874), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/629 (58%), Positives = 471/629 (74%), Gaps = 14/629 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 148  FGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLN 207

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N     T+ ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 208  DMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 267

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  A++I + ++ I  IVDG 
Sbjct: 268  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRLANEIREGKVVISTIVDGF 327

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK ++L +F  I+  F+K+ K
Sbjct: 328  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKRDALERFDRIAGMFEKVHK 387

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 388  IYDKEGYGTPAYVKAQEALSEELMTIRFTAKTIEKLCDLVRTQVDDVRKKERELRRIIVD 447

Query: 1110 KCGMPRLHFIKVF----------PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            KCG P+  FI+ F            N +NL WV+ +      ++ +L RNIP ++ELQQ+
Sbjct: 448  KCGFPQDEFIRDFSGYDKNGNRIASNLLNLKWVEKQAAAGKPWSAVLARNIPPVQELQQR 507

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L ++Q+ +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 508  LADIQSRVVVPLTQLKDINKRMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLD 567

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 568  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 627

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 628  NRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 687

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVT
Sbjct: 688  EDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVT 747

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKL+HPSR  KL+ F++
Sbjct: 748  RERIRQIEAKALRKLKHPSRSDKLRSFID 776



 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/634 (57%), Positives = 469/634 (73%), Gaps = 14/634 (2%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 130 KPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHL 189

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL+L+N     T+ ++ EE  EAALSTV
Sbjct: 190 PDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTV 249

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 250 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRL 309

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  IVDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 310 ANEIREGKVVISTIVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKR 369

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  I+  F+K+ K ++KEGY + +Y+KA   +S E++ IRFTAK+IEKLCD +R 
Sbjct: 370 DALERFDRIAGMFEKVHKIYDKEGYGTPAYVKAQEALSEELMTIRFTAKTIEKLCDLVRT 429

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVF----------PENEINLNWVDNETKIQHD 351
           Q++ V + E+++  I+V+KCG P+  FI+ F            N +NL WV+ +      
Sbjct: 430 QVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGNRIASNLLNLKWVEKQAAAGKP 489

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           ++ +L RNIP ++ELQQ+L ++Q+ +V+PL  L+DIN++M  GE  +R AK+EM EANLR
Sbjct: 490 WSAVLARNIPPVQELQQRLADIQSRVVVPLTQLKDINKRMNEGESSSRDAKKEMIEANLR 549

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 550 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 609

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+
Sbjct: 610 QARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPI 669

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGI
Sbjct: 670 SMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGI 729

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKL+
Sbjct: 730 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 763


>gi|331001176|ref|ZP_08324803.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
            YIT 11859]
 gi|329569108|gb|EGG50900.1| RNA polymerase sigma factor RpoD [Parasutterella excrementihominis
            YIT 11859]
          Length = 814

 Score =  726 bits (1873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/654 (57%), Positives = 480/654 (73%), Gaps = 20/654 (3%)

Query: 788  LFLPDKYDPDSYIRKFG-YKIFSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYL 846
            + + + Y P + +R  G  +  + K A +     +  ++ E    K K LI++GKERGYL
Sbjct: 171  VAIAESYVPPASVRGKGKARDKAMKEALNRSYAHHEEDDKETRLNKLKALIRMGKERGYL 230

Query: 847  TFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEA 903
            T+SE+ND +PE+I+D + I+ II T   + I V E     + L++ +     SDD  EE 
Sbjct: 231  TYSEVNDHMPENIVDPDQIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEE 290

Query: 904  TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPT 963
             EAAL+TVDS+FGRT DP++MYMREMGSVELLTR+GEIEIAKRIE+GLK M+HAIS CPT
Sbjct: 291  AEAALATVDSEFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPT 350

Query: 964  TIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD--- 1020
            TI+ IL  A+K+    ++ID+IVDGL+D           G      E++  +  S D   
Sbjct: 351  TIVAILEDAEKVRNGTMQIDQIVDGLVD-----------GLDEEASEQVAEDDESTDIGA 399

Query: 1021 --LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 1078
              ++  Q+++LK   L K  +    +  ++ A+E EGY S ++IKA + I  E+L +RFT
Sbjct: 400  SGMTAGQIDELKTVVLAKLDHCKELYQDLKHAYEAEGYRSPAFIKAQDAIQEELLSLRFT 459

Query: 1079 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 1138
            A ++E+LC  L+ Q+ +V + E +I +IVVN+  MPR  F+K F +NE NL W     + 
Sbjct: 460  ANTVERLCTMLKTQVEEVRKYESRIYDIVVNRAKMPRELFLKEFLDNETNLAWSQAIAES 519

Query: 1139 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 1198
               Y + + R +P I+ LQQ+L N+Q  + LPL DL+D+  +M  GE KARKAKREMTEA
Sbjct: 520  DKPYAIDVKRKLPEIQHLQQQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEA 579

Query: 1199 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 1258
            NLRLVISIAKKYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 580  NLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 639

Query: 1259 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 1318
            IADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KM+MPE+KIRKI+KIAK
Sbjct: 640  IADQARTIRIPVHMIETINKMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAK 699

Query: 1319 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 1378
            EP+SME+P+GDDEDSHLGDF+ED   +AP++AA  +S+  + K++L+SLTPRE+KVLRMR
Sbjct: 700  EPISMETPIGDDEDSHLGDFLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMR 759

Query: 1379 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            FGIEMS+DHTLEEVG+QFDVTRERIRQIEAKALRKLRHPSR  KLK F+EG  N
Sbjct: 760  FGIEMSTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFMEGGSN 813



 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/620 (58%), Positives = 461/620 (74%), Gaps = 19/620 (3%)

Query: 14  KTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE 73
           K ++  +K A +     +  ++ E    K K LI++GKERGYLT+SE+ND +PE+I+D +
Sbjct: 188 KARDKAMKEALNRSYAHHEEDDKETRLNKLKALIRMGKERGYLTYSEVNDHMPENIVDPD 247

Query: 74  IIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKD 130
            I+ II T   + I V E     + L++ +     SDD  EE  EAAL+TVDS+FGRT D
Sbjct: 248 QIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDSEFGRTTD 307

Query: 131 PIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEI 190
           P++MYMREMGSVELLTR+GEIEIAKRIE+GLK M+HAIS CPTTI+ IL  A+K+    +
Sbjct: 308 PVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAEKVRNGTM 367

Query: 191 KIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD-----LSTEQLEKLKYESLI 245
           +ID+IVDGL+D           G      E++  +  S D     ++  Q+++LK   L 
Sbjct: 368 QIDQIVDGLVD-----------GLDEEASEQVAEDDESTDIGASGMTAGQIDELKTVVLA 416

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           K  +    +  ++ A+E EGY S ++IKA + I  E+L +RFTA ++E+LC  L+ Q+ +
Sbjct: 417 KLDHCKELYQDLKHAYEAEGYRSPAFIKAQDAIQEELLSLRFTANTVERLCTMLKTQVEE 476

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V + E +I +IVVN+  MPR  F+K F +NE NL W     +    Y + + R +P I+ 
Sbjct: 477 VRKYESRIYDIVVNRAKMPRELFLKEFLDNETNLAWSQAIAESDKPYAIDVKRKLPEIQH 536

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
           LQQ+L N+Q  + LPL DL+D+  +M  GE KARKAKREMTEANLRLVISIAKKYT+RGL
Sbjct: 537 LQQQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGL 596

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 597 QFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 656

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQILQETG EPDP+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDDEDSHL
Sbjct: 657 INKMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHL 716

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDF+ED   +AP++AA  +S+  + K++L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG+Q
Sbjct: 717 GDFLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQ 776

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 777 FDVTRERIRQIEAKALRKLR 796


>gi|303257749|ref|ZP_07343761.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
 gi|302859719|gb|EFL82798.1| RNA polymerase sigma factor RpoD [Burkholderiales bacterium 1_1_47]
          Length = 814

 Score =  725 bits (1872), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/654 (57%), Positives = 480/654 (73%), Gaps = 20/654 (3%)

Query: 788  LFLPDKYDPDSYIRKFG-YKIFSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYL 846
            + + + Y P + +R  G  +  + K A +     +  ++ E    K K LI++GKERGYL
Sbjct: 171  VAIAESYVPPASVRGKGKARDKAMKEALNRSYAHHEEDDKETRLNKLKALIRMGKERGYL 230

Query: 847  TFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEA 903
            T+SE+ND +PE+I+D + I+ II T   + I V E     + L++ +     SDD  EE 
Sbjct: 231  TYSEVNDHMPENIVDPDQIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEE 290

Query: 904  TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPT 963
             EAAL+TVDS+FGRT DP++MYMREMGSVELLTR+GEIEIAKRIE+GLK M+HAIS CPT
Sbjct: 291  AEAALATVDSEFGRTTDPVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPT 350

Query: 964  TIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD--- 1020
            TI+ IL  A+K+    ++ID+IVDGL+D           G      E++  +  S D   
Sbjct: 351  TIVAILEDAEKVRNGTMQIDQIVDGLVD-----------GLDEEASEQVAEDDESTDIGA 399

Query: 1021 --LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 1078
              ++  Q+++LK   L K  +    +  ++ A+E EGY S ++IKA + I  E+L +RFT
Sbjct: 400  SGMTAGQIDELKTVVLAKLDHCKELYQDLKHAYEAEGYRSPAFIKAQDAIQEELLSLRFT 459

Query: 1079 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 1138
            A ++E+LC  L+ Q+ +V + E +I +IVVN+  MPR  F+K F +NE NL W     + 
Sbjct: 460  ANTVERLCTMLKTQVEEVRKYESRIYDIVVNRAKMPRELFLKEFLDNETNLAWSQAIAES 519

Query: 1139 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 1198
               Y + + R +P I+ LQQ+L N+Q  + LPL DL+D+  +M  GE KARKAKREMTEA
Sbjct: 520  DKPYAIDVKRKLPEIQHLQQQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEA 579

Query: 1199 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 1258
            NLRLVISIAKKYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 580  NLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 639

Query: 1259 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 1318
            IADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KM+MPE+KIRKI+KIAK
Sbjct: 640  IADQARTIRIPVHMIETINKMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAK 699

Query: 1319 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 1378
            EP+SME+P+GDDEDSHLGDF+ED   +AP++AA  +S+  + K++L+SLTPRE+KVLRMR
Sbjct: 700  EPISMETPIGDDEDSHLGDFLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMR 759

Query: 1379 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            FGIEMS+DHTLEEVG+QFDVTRERIRQIEAKALRKLRHPSR  KLK F+EG  N
Sbjct: 760  FGIEMSTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFMEGGSN 813



 Score =  702 bits (1813), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/620 (58%), Positives = 461/620 (74%), Gaps = 19/620 (3%)

Query: 14  KTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE 73
           K ++  +K A +     +  ++ E    K K LI++GKERGYLT+SE+ND +PE+I+D +
Sbjct: 188 KARDKAMKEALNRSYAHHEEDDKETRLNKLKALIRMGKERGYLTYSEVNDHMPENIVDPD 247

Query: 74  IIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKD 130
            I+ II T   + I V E     + L++ +     SDD  EE  EAAL+TVDS+FGRT D
Sbjct: 248 QIDQIISTLADLGIQVYEQAPTADDLLIGDSVPTASDDAAEEEAEAALATVDSEFGRTTD 307

Query: 131 PIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEI 190
           P++MYMREMGSVELLTR+GEIEIAKRIE+GLK M+HAIS CPTTI+ IL  A+K+    +
Sbjct: 308 PVRMYMREMGSVELLTREGEIEIAKRIEDGLKHMVHAISGCPTTIVAILEDAEKVRNGTM 367

Query: 191 KIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD-----LSTEQLEKLKYESLI 245
           +ID+IVDGL+D           G      E++  +  S D     ++  Q+++LK   L 
Sbjct: 368 QIDQIVDGLVD-----------GLDEEASEQVAEDDESTDIGASGMTAGQIDELKTVVLA 416

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           K  +    +  ++ A+E EGY S ++IKA + I  E+L +RFTA ++E+LC  L+ Q+ +
Sbjct: 417 KLDHCKELYQDLKHAYEAEGYRSPAFIKAQDAIQEELLSLRFTANTVERLCTMLKTQVEE 476

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V + E +I +IVVN+  MPR  F+K F +NE NL W     +    Y + + R +P I+ 
Sbjct: 477 VRKYESRIYDIVVNRAKMPRELFLKEFLDNETNLAWSQAIAESDKPYAIDVKRKLPEIQH 536

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
           LQQ+L N+Q  + LPL DL+D+  +M  GE KARKAKREMTEANLRLVISIAKKYT+RGL
Sbjct: 537 LQQQLQNIQNAVTLPLKDLKDVYNQMATGEAKARKAKREMTEANLRLVISIAKKYTNRGL 596

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 597 QFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 656

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQILQETG EPDP+ +A KM+MPE+KIRKI+KIAKEP+SME+P+GDDEDSHL
Sbjct: 657 INKMNRISRQILQETGVEPDPAELAEKMDMPEDKIRKILKIAKEPISMETPIGDDEDSHL 716

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDF+ED   +AP++AA  +S+  + K++L+SLTPRE+KVLRMRFGIEMS+DHTLEEVG+Q
Sbjct: 717 GDFLEDFGTVAPAEAAQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQ 776

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 777 FDVTRERIRQIEAKALRKLR 796


>gi|34499217|ref|NP_903432.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
            12472]
 gi|34105068|gb|AAQ61424.1| RNA polymerase sigma factor RpoD [Chromobacterium violaceum ATCC
            12472]
          Length = 643

 Score =  725 bits (1871), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/630 (58%), Positives = 475/630 (75%), Gaps = 16/630 (2%)

Query: 817  DIKSNSRE--EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 874
            D+K + +E   +E  RK+ + LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10   DVKDSQQEVMSLEEQRKRLRQLIALGKERGYLTYAEINDHLPEDVSDAEQIENIVTMIAG 69

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 931
            + I V E   D ETL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70   LGIQVCEEAPDAETLLMSDATPSVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 932  VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 991
            VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   ++++++EI++DE+VDG ID
Sbjct: 130  VELLTREGEIEIAKRIEDGLKYMIQAISACPGTIAEVLELMERVARDEIRVDEVVDGFID 189

Query: 992  KNFSSNNRVIKGNKNNNEEKILIESSSADLST-----------EQLEKLKYESLIKFSNI 1040
             N  + +        ++++ +  E    +                LE+LK ++L  F+ +
Sbjct: 190  LNAPTEDEAQFAEPEDSDDLLDEEEEEEEDEDGAPVDADADAAANLEELKQQALEHFAGV 249

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
               FDKM KA   +G  S+ Y++  + I+ E + +RF  + +E LC++LR ++N++   E
Sbjct: 250  RMLFDKMVKALNAKGQQSKEYLELQDAITTEFMLVRFATRQVESLCESLRGRVNEIRTYE 309

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + I +I V++  M R HFIKVFP NE NL+WV+NE      ++  L R   +I E Q +L
Sbjct: 310  RDIQDICVSRVRMDRAHFIKVFPGNETNLDWVENEIDSGKAWSEALTRFKHAIIEKQTRL 369

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
             +LQ   +L +  L++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 370  SDLQDKAMLSIKALKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDL 429

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 430  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 489

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQE+G EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIE
Sbjct: 490  RISRQILQESGREPDPAELAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIE 549

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D+N LAPSDAA+ +S++   K++L++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 550  DQNNLAPSDAAMYSSLKDATKEVLDTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 609

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            ERIRQIEAKALRKLRHP+R  +L+ FL+ +
Sbjct: 610  ERIRQIEAKALRKLRHPTRSERLRSFLDSE 639



 Score =  710 bits (1832), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/615 (58%), Positives = 464/615 (75%), Gaps = 16/615 (2%)

Query: 27  DIKSNSRE--EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 84
           D+K + +E   +E  RK+ + LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10  DVKDSQQEVMSLEEQRKRLRQLIALGKERGYLTYAEINDHLPEDVSDAEQIENIVTMIAG 69

Query: 85  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 141
           + I V E   D ETL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70  LGIQVCEEAPDAETLLMSDATPSVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 142 VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 201
           VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   ++++++EI++DE+VDG ID
Sbjct: 130 VELLTREGEIEIAKRIEDGLKYMIQAISACPGTIAEVLELMERVARDEIRVDEVVDGFID 189

Query: 202 KNFSSNNRVIKGNKNNNEEKILIESSSADLST-----------EQLEKLKYESLIKFSNI 250
            N  + +        ++++ +  E    +                LE+LK ++L  F+ +
Sbjct: 190 LNAPTEDEAQFAEPEDSDDLLDEEEEEEEDEDGAPVDADADAAANLEELKQQALEHFAGV 249

Query: 251 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
              FDKM KA   +G  S+ Y++  + I+ E + +RF  + +E LC++LR ++N++   E
Sbjct: 250 RMLFDKMVKALNAKGQQSKEYLELQDAITTEFMLVRFATRQVESLCESLRGRVNEIRTYE 309

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           + I +I V++  M R HFIKVFP NE NL+WV+NE      ++  L R   +I E Q +L
Sbjct: 310 RDIQDICVSRVRMDRAHFIKVFPGNETNLDWVENEIDSGKAWSEALTRFKHAIIEKQTRL 369

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
            +LQ   +L +  L++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 370 SDLQDKAMLSIKALKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDL 429

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 430 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 489

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQILQE+G EPDP+ +A KMEMPEEKIRKIMKI+KEP+SME+P+GDD+DSHLGDFIE
Sbjct: 490 RISRQILQESGREPDPAELAEKMEMPEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIE 549

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D+N LAPSDAA+ +S++   K++L++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 550 DQNNLAPSDAAMYSSLKDATKEVLDTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 609

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 610 ERIRQIEAKALRKLR 624


>gi|388565442|ref|ZP_10151933.1| RNA polymerase sigma-70 subunit RpoD [Hydrogenophaga sp. PBC]
 gi|388267331|gb|EIK92830.1| RNA polymerase sigma-70 subunit RpoD [Hydrogenophaga sp. PBC]
          Length = 791

 Score =  723 bits (1865), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/600 (59%), Positives = 456/600 (76%), Gaps = 4/600 (0%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LIKLGK RGYLT  EIND LP+ +++ E +E ++     M ++V E   D ETL+L+
Sbjct: 190  LKTLIKLGKTRGYLTHGEINDHLPDKLVEAETLEVVVSLLNDMGVAVYEQTPDAETLLLN 249

Query: 893  NITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            N       EE  E      LSTVDS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE
Sbjct: 250  NTGPTAATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIE 309

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
             GL  M+ AIS  P TI EIL  A++I + ++ I  +VDG  D + + +    +   + +
Sbjct: 310  GGLHSMMEAISESPATIAEILAMAEEIREGKVVISTVVDGFADADEADDYVAEEDFDDYD 369

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 1068
            E         +   T +LE+LK E+L +F  +   F+K+ K ++KEGY    Y+K    I
Sbjct: 370  EADDDDGKGGSKALTRKLEELKREALERFDALRGMFEKLHKTYDKEGYGGAVYVKTQQAI 429

Query: 1069 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 1128
            + +++ IRFTAK+IEKLC T+R Q++++ + E+++  I+V+KCGMP+  FIK FP N +N
Sbjct: 430  TEKLMTIRFTAKAIEKLCSTVRGQVDEIRKKERELRRIIVDKCGMPQETFIKDFPPNLLN 489

Query: 1129 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
            L WV+ +      +++I+ RNIP ++ELQQ LI++Q  +V+P++ L+DI+++M  GE  +
Sbjct: 490  LKWVEKQAAAGKPWSVIIERNIPPVQELQQGLIDIQNSVVVPIDHLKDIHKRMNNGEASS 549

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            R AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 550  RDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 609

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G EPD S++A KMEMPE+
Sbjct: 610  WWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASILAEKMEMPED 669

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED    AP +AA+ A +R VVK+IL+SLT
Sbjct: 670  KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTTNTAPIEAAMQAGLREVVKEILDSLT 729

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            PRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRERIRQIE+KA+RKL+HPSR  KL+ F++
Sbjct: 730  PREAKVLRMRFGIEMSNDHTLEEVGKQFDVTRERIRQIESKAVRKLKHPSRSDKLRSFID 789



 Score =  712 bits (1837), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/624 (57%), Positives = 462/624 (74%), Gaps = 4/624 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S EE    R++ K LIKLGK RGYLT  EIND L
Sbjct: 153 KPLRMKISKAKERALMKEFGLDETILSEEEARARRERLKTLIKLGKTRGYLTHGEINDHL 212

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ +++ E +E ++     M ++V E   D ETL+L+N       EE  E      LSTV
Sbjct: 213 PDKLVEAETLEVVVSLLNDMGVAVYEQTPDAETLLLNNTGPTAATEEEAEEEAEAALSTV 272

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS  P TI EIL  
Sbjct: 273 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLHSMMEAISESPATIAEILAM 332

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  +VDG  D + + +    +   + +E         +   T +LE+LK 
Sbjct: 333 AEEIREGKVVISTVVDGFADADEADDYVAEEDFDDYDEADDDDGKGGSKALTRKLEELKR 392

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +   F+K+ K ++KEGY    Y+K    I+ +++ IRFTAK+IEKLC T+R 
Sbjct: 393 EALERFDALRGMFEKLHKTYDKEGYGGAVYVKTQQAITEKLMTIRFTAKAIEKLCSTVRG 452

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
           Q++++ + E+++  I+V+KCGMP+  FIK FP N +NL WV+ +      +++I+ RNIP
Sbjct: 453 QVDEIRKKERELRRIIVDKCGMPQETFIKDFPPNLLNLKWVEKQAAAGKPWSVIIERNIP 512

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            ++ELQQ LI++Q  +V+P++ L+DI+++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 513 PVQELQQGLIDIQNSVVVPIDHLKDIHKRMNNGEASSRDAKKEMIEANLRLVISIAKKYT 572

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 573 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 632

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD S++A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 633 MIETINKMNRISRQHLQEFGFEPDASILAEKMEMPEDKIRKIMKIAKEPISMETPIGDDD 692

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVK+IL+SLTPRE+KVLRMRFGIEMS+DHTLEE
Sbjct: 693 DSHLGDFIEDTTNTAPIEAAMQAGLREVVKEILDSLTPREAKVLRMRFGIEMSNDHTLEE 752

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIE+KA+RKL+
Sbjct: 753 VGKQFDVTRERIRQIESKAVRKLK 776


>gi|239814768|ref|YP_002943678.1| RNA polymerase sigma-70 subunit RpoD [Variovorax paradoxus S110]
 gi|239801345|gb|ACS18412.1| RNA polymerase, sigma 70 subunit, RpoD [Variovorax paradoxus S110]
          Length = 754

 Score =  721 bits (1862), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/629 (58%), Positives = 469/629 (74%), Gaps = 14/629 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R + K LI LGK RGYLT  EI+D LP+ ++D E +E ++    
Sbjct: 124  FGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHLPDKLVDAETMEVVVTMLN 183

Query: 874  YMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N     T+ ++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 184  DMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 243

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  A  I + ++ I  +VDG 
Sbjct: 244  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRLAADIREGKVVISTVVDGF 303

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +EE        +   T++LE+LK ++L +F  I+  F+K+ K
Sbjct: 304  SNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKRDALERFDRIASMFEKVHK 363

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             ++KEGY + +Y KA   +S+E++ IRFTAK+IEKLCD +R Q++ V + E+++  I+V+
Sbjct: 364  IYDKEGYGTPAYEKAQQALSDELMTIRFTAKTIEKLCDLVRTQVDDVRKKERELRRIIVD 423

Query: 1110 KCGMPRLHFIKVF----------PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            KCG P+  FI+ F          P N +N  WV+ +      ++ +L RNIP ++ELQQK
Sbjct: 424  KCGFPQDEFIRDFSGYDKNGNRVPSNLLNQKWVEKQAAAGKPWSAVLARNIPPVQELQQK 483

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L ++Q+ +V+PL  L++IN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 484  LADIQSRVVVPLTQLKEINKRMNEGESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLD 543

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 544  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 603

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 604  NRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 663

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVT
Sbjct: 664  EDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVT 723

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKL+HPSR  KL+ F++
Sbjct: 724  RERIRQIEAKALRKLKHPSRSDKLRSFID 752



 Score =  712 bits (1837), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/634 (57%), Positives = 467/634 (73%), Gaps = 14/634 (2%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R + K LI LGK RGYLT  EI+D L
Sbjct: 106 KPLRMKISKAKERALMKEFGLDETVLSEEDLAKRRSRLKTLITLGKTRGYLTHGEISDHL 165

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI----TSDDDVEEATEAALSTV 121
           P+ ++D E +E ++     M ++V E   D ETL+L+N     T+ ++ EE  EAALSTV
Sbjct: 166 PDKLVDAETMEVVVTMLNDMGVAVYEQTPDAETLLLNNTAPTATTVEEAEEEAEAALSTV 225

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 226 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRL 285

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A  I + ++ I  +VDG  + N + +    +     +EE        +   T++LE+LK 
Sbjct: 286 AADIREGKVVISTVVDGFSNPNEADDYVAEEDFDEFDEEDDDDGKGGSKALTKKLEELKR 345

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  I+  F+K+ K ++KEGY + +Y KA   +S+E++ IRFTAK+IEKLCD +R 
Sbjct: 346 DALERFDRIASMFEKVHKIYDKEGYGTPAYEKAQQALSDELMTIRFTAKTIEKLCDLVRT 405

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVF----------PENEINLNWVDNETKIQHD 351
           Q++ V + E+++  I+V+KCG P+  FI+ F          P N +N  WV+ +      
Sbjct: 406 QVDDVRKKERELRRIIVDKCGFPQDEFIRDFSGYDKNGNRVPSNLLNQKWVEKQAAAGKP 465

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           ++ +L RNIP ++ELQQKL ++Q+ +V+PL  L++IN++M  GE  +R AK+EM EANLR
Sbjct: 466 WSAVLARNIPPVQELQQKLADIQSRVVVPLTQLKEINKRMNEGESSSRDAKKEMIEANLR 525

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 526 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 585

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQ LQE G EPD  ++A KME+PE+KIRKIMKIAKEP+
Sbjct: 586 QARTIRIPVHMIETINKMNRISRQHLQEFGFEPDAGILAAKMEIPEDKIRKIMKIAKEPI 645

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED +  AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGI
Sbjct: 646 SMETPIGDDDDSHLGDFIEDSSNTAPIEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGI 705

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EMS+DHTLEEVGKQFDVTRERIRQIEAKALRKL+
Sbjct: 706 EMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 739


>gi|74318406|ref|YP_316146.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
            denitrificans ATCC 25259]
 gi|74057901|gb|AAZ98341.1| Carbamoyl-phosphate synthase L chain, ATP-binding [Thiobacillus
            denitrificans ATCC 25259]
          Length = 656

 Score =  720 bits (1858), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/622 (57%), Positives = 464/622 (74%), Gaps = 4/622 (0%)

Query: 809  SKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESI 868
            +KK      +K  +  E E  R + K LI LGKERG+LT++EIND LP++++D + IE +
Sbjct: 31   AKKPEALLPLKELTPVEAEARRTQLKNLIILGKERGFLTYAEINDHLPDEVLDADQIEGV 90

Query: 869  IKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMY 925
            I     M I V +   D ETL++   +   +D+DV    E AL+TVDS+FGRT DP++MY
Sbjct: 91   ISMINDMGIQVYDEAPDAETLLMQEAAPAVADEDVVAEAEQALTTVDSEFGRTTDPVRMY 150

Query: 926  MREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEI 985
            MREMGSV+LLTR+GEIEIAKRIEEGL+ M+ AISSCP TI +IL  A ++ K+E++IDE+
Sbjct: 151  MREMGSVDLLTREGEIEIAKRIEEGLRHMVQAISSCPLTIQQILDMAAQVEKDELRIDEL 210

Query: 986  VDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
            +DG ++    +          ++E     E +SA ++   L +LK E+L +F  I   + 
Sbjct: 211  IDGFVEAETEAAAEEET-AAGDDETDEDDEDASAAVAAANLAQLKAEALAQFDYIRKAYK 269

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K + A  K G  S  ++KA   ++  ++ IRF+ + ++ LC+ +R+ + +V   E++I+E
Sbjct: 270  KAQNAHVKYGLGSAQHMKAQAEVTELLMAIRFSVRQVDNLCEQIRSAVEEVRSHERKIME 329

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              VN+ GMPR HFIK FP NE NL W+D E   +  Y   L +    +K  Q+ LI +Q 
Sbjct: 330  FCVNRSGMPRAHFIKAFPGNETNLAWLDREIAAKKAYCSTLSKVQYEVKAHQEALIAMQD 389

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LP+ +L+DIN++M  GE KAR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 390  RVGLPIKNLKDINKQMSTGEAKARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 449

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 450  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 509

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQETG EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDDEDSHLGDFIED + L
Sbjct: 510  ILQETGIEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDASTL 569

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P D+A+ A++R   +++L+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQ
Sbjct: 570  SPDDSAIYANLRDATREVLDSLTSREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQ 629

Query: 1406 IEAKALRKLRHPSRYYKLKIFL 1427
            IEAKALRKLRHP+R  KLK F+
Sbjct: 630  IEAKALRKLRHPTRSEKLKSFV 651



 Score =  704 bits (1818), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 354/623 (56%), Positives = 458/623 (73%), Gaps = 4/623 (0%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K   ++ +K      K      +K  +  E E  R + K LI LGKERG+LT++EIND L
Sbjct: 18  KPVAVRGRKPGGGAKKPEALLPLKELTPVEAEARRTQLKNLIILGKERGFLTYAEINDHL 77

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVD 122
           P++++D + IE +I     M I V +   D ETL++   +   +D+DV    E AL+TVD
Sbjct: 78  PDEVLDADQIEGVISMINDMGIQVYDEAPDAETLLMQEAAPAVADEDVVAEAEQALTTVD 137

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMGSV+LLTR+GEIEIAKRIEEGL+ M+ AISSCP TI +IL  A
Sbjct: 138 SEFGRTTDPVRMYMREMGSVDLLTREGEIEIAKRIEEGLRHMVQAISSCPLTIQQILDMA 197

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 242
            ++ K+E++IDE++DG ++    +          ++E     E +SA ++   L +LK E
Sbjct: 198 AQVEKDELRIDELIDGFVEAETEAAAEEET-AAGDDETDEDDEDASAAVAAANLAQLKAE 256

Query: 243 SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 302
           +L +F  I   + K + A  K G  S  ++KA   ++  ++ IRF+ + ++ LC+ +R+ 
Sbjct: 257 ALAQFDYIRKAYKKAQNAHVKYGLGSAQHMKAQAEVTELLMAIRFSVRQVDNLCEQIRSA 316

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E++I+E  VN+ GMPR HFIK FP NE NL W+D E   +  Y   L +    
Sbjct: 317 VEEVRSHERKIMEFCVNRSGMPRAHFIKAFPGNETNLAWLDREIAAKKAYCSTLSKVQYE 376

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           +K  Q+ LI +Q  + LP+ +L+DIN++M  GE KAR+AKREM EANLRLVISIAKKYT+
Sbjct: 377 VKAHQEALIAMQDRVGLPIKNLKDINKQMSTGEAKARRAKREMIEANLRLVISIAKKYTN 436

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 437 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 496

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQILQETG EPDP+ +AIKMEMPE+KIRKIMKIAKEP+SME+P+GDDED
Sbjct: 497 IETINKMNRISRQILQETGIEPDPATLAIKMEMPEDKIRKIMKIAKEPISMETPIGDDED 556

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED + L+P D+A+ A++R   +++L+SLT RE+KVLRMRFGIEM++DHTLEEV
Sbjct: 557 SHLGDFIEDASTLSPDDSAIYANLRDATREVLDSLTSREAKVLRMRFGIEMNTDHTLEEV 616

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 617 GKQFDVTRERIRQIEAKALRKLR 639


>gi|254000081|ref|YP_003052144.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus glucosetrophus
            SIP3-4]
 gi|313202040|ref|YP_004040698.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. MP688]
 gi|253986760|gb|ACT51617.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus glucosetrophus
            SIP3-4]
 gi|312441356|gb|ADQ85462.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. MP688]
          Length = 638

 Score =  719 bits (1857), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/611 (59%), Positives = 456/611 (74%), Gaps = 12/611 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EIND LP+D+ D E I+ II     M I V E   D E L
Sbjct: 24   RTRLKSLIVLGKERGYLTYAEINDHLPDDVQDSEQIDGIIGMINDMGIQVYEETPDAEAL 83

Query: 890  MLSNI---TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            ++S+     +D+D  E  E ALSTVDS+FGRT DP++MYMREMG+V+LLTR+GEIEIAKR
Sbjct: 84   LMSDAPPPVADEDAVEEAEQALSTVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKR 143

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV------ 1000
            IE+GLK M+ AI++CPTTI E+L   +K+ K+E+ +D++VDGLID +      +      
Sbjct: 144  IEDGLKHMVQAIAACPTTIAELLAMVEKVEKDELSVDDLVDGLIDSDVGLEEDIPVEAAE 203

Query: 1001 ---IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +   +  ++     + +A +S E L KLK E L +F+ I     KM    ++ G  
Sbjct: 204  AEEEEPEDDEEDDGDEDGAKAAAISAEALAKLKEEVLTRFAVIRQSHQKMTVILQERGSQ 263

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             + Y    N I  E+   RF+AK +E LCD +RN + ++   E++I+E  V+K GMPR H
Sbjct: 264  DKEYQALQNAILEELTAFRFSAKQVEALCDQVRNMVEEIRGHERKIMEFCVDKSGMPRAH 323

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FIKVFP NE NL+W+  E  +   Y   L R   SI + QQ+L++LQ  + +P+ +L++I
Sbjct: 324  FIKVFPGNEGNLDWLAGELTVNKPYVERLERFKHSIVDQQQRLLDLQDRVGIPIKELKEI 383

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N++M  GE +AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 384  NKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 443

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+
Sbjct: 444  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPA 503

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A KMEMPE+KIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP DAA+ AS+R
Sbjct: 504  TLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDMTTLAPVDAAVYASLR 563

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               K++L SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 564  EATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 623

Query: 1418 SRYYKLKIFLE 1428
            +R  +L+ FLE
Sbjct: 624  TRSERLRSFLE 634



 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/598 (59%), Positives = 446/598 (74%), Gaps = 12/598 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EIND LP+D+ D E I+ II     M I V E   D E L
Sbjct: 24  RTRLKSLIVLGKERGYLTYAEINDHLPDDVQDSEQIDGIIGMINDMGIQVYEETPDAEAL 83

Query: 100 MLSNI---TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           ++S+     +D+D  E  E ALSTVDS+FGRT DP++MYMREMG+V+LLTR+GEIEIAKR
Sbjct: 84  LMSDAPPPVADEDAVEEAEQALSTVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKR 143

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV------ 210
           IE+GLK M+ AI++CPTTI E+L   +K+ K+E+ +D++VDGLID +      +      
Sbjct: 144 IEDGLKHMVQAIAACPTTIAELLAMVEKVEKDELSVDDLVDGLIDSDVGLEEDIPVEAAE 203

Query: 211 ---IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
               +   +  ++     + +A +S E L KLK E L +F+ I     KM    ++ G  
Sbjct: 204 AEEEEPEDDEEDDGDEDGAKAAAISAEALAKLKEEVLTRFAVIRQSHQKMTVILQERGSQ 263

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            + Y    N I  E+   RF+AK +E LCD +RN + ++   E++I+E  V+K GMPR H
Sbjct: 264 DKEYQALQNAILEELTAFRFSAKQVEALCDQVRNMVEEIRGHERKIMEFCVDKSGMPRAH 323

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIKVFP NE NL+W+  E  +   Y   L R   SI + QQ+L++LQ  + +P+ +L++I
Sbjct: 324 FIKVFPGNEGNLDWLAGELTVNKPYVERLERFKHSIVDQQQRLLDLQDRVGIPIKELKEI 383

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N++M  GE +AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 384 NKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 443

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+
Sbjct: 444 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPA 503

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A KMEMPE+KIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP DAA+ AS+R
Sbjct: 504 TLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDMTTLAPVDAAVYASLR 563

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              K++L SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 564 EATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 621


>gi|332528540|ref|ZP_08404528.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
            19624]
 gi|332042051|gb|EGI78389.1| RNA polymerase, sigma 70 subunit, rpod [Hylemonella gracilis ATCC
            19624]
          Length = 784

 Score =  718 bits (1854), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/627 (56%), Positives = 462/627 (73%), Gaps = 14/627 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R++ K+LIKLGK RGYLT  EI+D LP+ + D E +E ++    
Sbjct: 154  FGLDETVLSEEDLAKRRERLKLLIKLGKTRGYLTHGEISDHLPDKLADAETLEVVVAMLS 213

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+++N       EE  E      +STVDS+FGRT DP++MYMREM
Sbjct: 214  DMGVTVFEQTPDAETLLINNTAPTAASEEEAEEEAEAAVSTVDSEFGRTTDPVRMYMREM 273

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL DM+ AIS+ PTTI  +L  A++I + ++ I  +VDG 
Sbjct: 274  GTVELLTREGEIEIAKRIEGGLMDMMEAISASPTTIAALLAMAEEIREGKVVISTVVDGF 333

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            ++   S +    +     +E         +   T++LE+LK ++L +F  I   F+K+ K
Sbjct: 334  VNAEESDDYVAEEDFDEYDEADDDDGKGGSKALTKKLEELKNQALERFDRIRSMFEKVHK 393

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A++KEGY + +Y+KA   +S+E++ IRFTAK+IEKLCD +R Q+  V   E+++  I+V+
Sbjct: 394  AYDKEGYGTPAYVKAQKALSDELMTIRFTAKTIEKLCDLVRGQVADVRHKERELRRIIVD 453

Query: 1110 KCGMPRLHFIKVFPENE----------INLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            +CG P+  F+  F   +          ++L WV+ +      ++ I+ RN+P I+++QQK
Sbjct: 454  RCGYPQDQFVLEFGGRDKNGNPSKSHLLDLKWVEKQANAGKPWSGIISRNVPPIQDIQQK 513

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            LI+LQ  +V+PL  L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 514  LIDLQARVVVPLEQLKDINKRMNQGEAASRAAKKEMIEANLRLVISIAKKYTNRGLQFLD 573

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 574  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 633

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 634  NRISRQHLQEFGFEPDASLLAQKMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 693

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED    AP +AA+ A +R VVK+IL+ LTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVT
Sbjct: 694  EDTANTAPVEAAMQAGLREVVKEILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVT 753

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIF 1426
            RERIRQIEAKALRKL+HPSR  KL+ F
Sbjct: 754  RERIRQIEAKALRKLKHPSRSDKLRSF 780



 Score =  711 bits (1835), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/634 (56%), Positives = 462/634 (72%), Gaps = 14/634 (2%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  +IK  K KE  L   F  D    S E++   R++ K+LIKLGK RGYLT  EI+D L
Sbjct: 136 KPLRIKVSKAKERALMKEFGLDETVLSEEDLAKRRERLKLLIKLGKTRGYLTHGEISDHL 195

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ + D E +E ++     M ++V E   D ETL+++N       EE  E      +STV
Sbjct: 196 PDKLADAETLEVVVAMLSDMGVTVFEQTPDAETLLINNTAPTAASEEEAEEEAEAAVSTV 255

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ PTTI  +L  
Sbjct: 256 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPTTIAALLAM 315

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I + ++ I  +VDG ++   S +    +     +E         +   T++LE+LK 
Sbjct: 316 AEEIREGKVVISTVVDGFVNAEESDDYVAEEDFDEYDEADDDDGKGGSKALTKKLEELKN 375

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           ++L +F  I   F+K+ KA++KEGY + +Y+KA   +S+E++ IRFTAK+IEKLCD +R 
Sbjct: 376 QALERFDRIRSMFEKVHKAYDKEGYGTPAYVKAQKALSDELMTIRFTAKTIEKLCDLVRG 435

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE----------INLNWVDNETKIQHD 351
           Q+  V   E+++  I+V++CG P+  F+  F   +          ++L WV+ +      
Sbjct: 436 QVADVRHKERELRRIIVDRCGYPQDQFVLEFGGRDKNGNPSKSHLLDLKWVEKQANAGKP 495

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           ++ I+ RN+P I+++QQKLI+LQ  +V+PL  L+DIN++M  GE  +R AK+EM EANLR
Sbjct: 496 WSGIISRNVPPIQDIQQKLIDLQARVVVPLEQLKDINKRMNQGEAASRAAKKEMIEANLR 555

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 556 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 615

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQ LQE G EPD S++A KME+PE+KIRKIMKIAKEP+
Sbjct: 616 QARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASLLAQKMEIPEDKIRKIMKIAKEPI 675

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED    AP +AA+ A +R VVK+IL+ LTPRE+KVLRMRFGI
Sbjct: 676 SMETPIGDDDDSHLGDFIEDTANTAPVEAAMQAGLREVVKEILDGLTPREAKVLRMRFGI 735

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EM+SDHTLEEVGKQFDVTRERIRQIEAKALRKL+
Sbjct: 736 EMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLK 769


>gi|89900350|ref|YP_522821.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
 gi|89345087|gb|ABD69290.1| sigma 70 (RpoD) [Rhodoferax ferrireducens T118]
          Length = 783

 Score =  718 bits (1854), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/627 (57%), Positives = 460/627 (73%), Gaps = 14/627 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F  D    S E++   R++ K LIKLGK RGYLT  EI+D LP+ ++D E +E +I    
Sbjct: 153  FGLDETVLSEEDMAKRRQRLKALIKLGKTRGYLTHGEISDHLPDKLVDAETLEVVISMLN 212

Query: 874  YMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTVDSDFGRTKDPIKMYMREM 929
             M ++V E   D ETL+L+N  S    EE  E      LSTVDS+FGRT DP++MYMREM
Sbjct: 213  DMGVAVYEQTPDAETLLLNNNVSTAATEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 272

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  ++ I + ++ I  IVDG 
Sbjct: 273  GTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRLSEDIREGKVVITTIVDGF 332

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + N + +    +     +          +   T++LE+LK E+L +F  +   F+K+  
Sbjct: 333  SNPNEADDYVAEEDFDEFDAADDDDGKGGSKALTKKLEELKNEALSRFDRLRELFEKIHT 392

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             + KEGY + SYIK    +S E++ IRFTAK+IEKLCD +R+Q++ V + E+++  I+V+
Sbjct: 393  IYNKEGYGTPSYIKTQKALSEELMSIRFTAKTIEKLCDLVRSQVDDVRKKERELRRIIVD 452

Query: 1110 KCGMPRLHFIKVFPENE----------INLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            KCG P+ +FI  F   +          +NL W++ +      +  I+ RNIP +++LQQK
Sbjct: 453  KCGYPQENFIADFSGRDKHGNKVASQLLNLKWIEKQAASGKHWGPIMARNIPPVQDLQQK 512

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L +LQ+ +V+PL+ L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 513  LTDLQSKVVVPLDQLKDINKRMNEGEYSSRAAKKEMIEANLRLVISIAKKYTNRGLQFLD 572

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 573  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKM 632

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ LQE G EPD SV+A +ME+PE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFI
Sbjct: 633  NRISRQHLQEFGFEPDASVLAERMEIPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFI 692

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEM+SDHTLEEVGKQFDVT
Sbjct: 693  EDAANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVT 752

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIF 1426
            RERIRQIEAKALRKL+HPSR  KL+ F
Sbjct: 753  RERIRQIEAKALRKLKHPSRSDKLRSF 779



 Score =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/634 (57%), Positives = 460/634 (72%), Gaps = 14/634 (2%)

Query: 6   KKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K  ++K  K KE  L   F  D    S E++   R++ K LIKLGK RGYLT  EI+D L
Sbjct: 135 KPLRMKISKAKERALMKEFGLDETVLSEEDMAKRRQRLKALIKLGKTRGYLTHGEISDHL 194

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAA----LSTV 121
           P+ ++D E +E +I     M ++V E   D ETL+L+N  S    EE  E      LSTV
Sbjct: 195 PDKLVDAETLEVVISMLNDMGVAVYEQTPDAETLLLNNNVSTAATEEEAEEEAEAALSTV 254

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GL  M+ AIS+ P TI EIL  
Sbjct: 255 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEGGLMAMMEAISASPATIAEILRL 314

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           ++ I + ++ I  IVDG  + N + +    +     +          +   T++LE+LK 
Sbjct: 315 SEDIREGKVVITTIVDGFSNPNEADDYVAEEDFDEFDAADDDDGKGGSKALTKKLEELKN 374

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           E+L +F  +   F+K+   + KEGY + SYIK    +S E++ IRFTAK+IEKLCD +R+
Sbjct: 375 EALSRFDRLRELFEKIHTIYNKEGYGTPSYIKTQKALSEELMSIRFTAKTIEKLCDLVRS 434

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE----------INLNWVDNETKIQHD 351
           Q++ V + E+++  I+V+KCG P+ +FI  F   +          +NL W++ +      
Sbjct: 435 QVDDVRKKERELRRIIVDKCGYPQENFIADFSGRDKHGNKVASQLLNLKWIEKQAASGKH 494

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           +  I+ RNIP +++LQQKL +LQ+ +V+PL+ L+DIN++M  GE  +R AK+EM EANLR
Sbjct: 495 WGPIMARNIPPVQDLQQKLTDLQSKVVVPLDQLKDINKRMNEGEYSSRAAKKEMIEANLR 554

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 555 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 614

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQ LQE G EPD SV+A +ME+PE+KIRKIMKIAKEP+
Sbjct: 615 QARTIRIPVHMIETINKMNRISRQHLQEFGFEPDASVLAERMEIPEDKIRKIMKIAKEPI 674

Query: 532 SMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGI 591
           SME+P+GDD+DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGI
Sbjct: 675 SMETPIGDDDDSHLGDFIEDAANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGI 734

Query: 592 EMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           EM+SDHTLEEVGKQFDVTRERIRQIEAKALRKL+
Sbjct: 735 EMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLK 768


>gi|347541209|ref|YP_004848635.1| RNA polymerase sigma-70 subunit RpoD [Pseudogulbenkiania sp. NH8B]
 gi|345644388|dbj|BAK78221.1| RNA polymerase, sigma-70 subunit, RpoD [Pseudogulbenkiania sp. NH8B]
          Length = 640

 Score =  718 bits (1853), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/625 (58%), Positives = 467/625 (74%), Gaps = 13/625 (2%)

Query: 817  DIKSNSREE--IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 874
            D++ N +E   +E+ RK+ ++LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10   DMQDNEQESMSLEDQRKRLRLLIALGKERGYLTYAEINDHLPEDVSDTEQIENIVTMITG 69

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 931
            + I V +   D +TL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70   LGIQVYDEAPDADTLLMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 932  VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 991
            VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   D++   +I++DE+VDG ID
Sbjct: 130  VELLTREGEIEIAKRIEDGLKHMIEAISACPGTISEVLALLDRVEAGDIRVDEVVDGFID 189

Query: 992  KNFSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYESLIKFSNISFH 1043
             N      V      + +E +  E    +        +S   LE+LK +SL  F+ +   
Sbjct: 190  PNAEVEEEVPFAEPVDPDEVLDEEEEEEEAEEEDAEAISNANLEELKLQSLEHFALVRAL 249

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            F+++     K+G  SE Y +    I+   + +RF  + IE LC++LR+++N++   E+ I
Sbjct: 250  FEELVVVLRKQGNQSEEYRQLQGAITESFMKVRFATRQIESLCESLRSRVNEIRSYERDI 309

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I V +  M R HFIK FP NEIN +WV++E      ++  L R   +I E Q KL  L
Sbjct: 310  QDICVTRVRMDRAHFIKYFPGNEINTDWVEDEISSGKPWSEALTRFKYAIIEKQTKLAEL 369

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            Q   +L + DL++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 370  QDRAMLSIKDLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 429

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 430  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 489

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQILQETG EPDP+ +A +MEMPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+N
Sbjct: 490  RQILQETGHEPDPAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQN 549

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             LAPSDAA+ +S++   K++L +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 550  NLAPSDAAMYSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 609

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHP+R  +L+ FL+
Sbjct: 610  RQIEAKALRKLRHPTRSERLRSFLD 634



 Score =  703 bits (1814), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/612 (58%), Positives = 457/612 (74%), Gaps = 13/612 (2%)

Query: 27  DIKSNSREE--IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 84
           D++ N +E   +E+ RK+ ++LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10  DMQDNEQESMSLEDQRKRLRLLIALGKERGYLTYAEINDHLPEDVSDTEQIENIVTMITG 69

Query: 85  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 141
           + I V +   D +TL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70  LGIQVYDEAPDADTLLMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 142 VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 201
           VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   D++   +I++DE+VDG ID
Sbjct: 130 VELLTREGEIEIAKRIEDGLKHMIEAISACPGTISEVLALLDRVEAGDIRVDEVVDGFID 189

Query: 202 KNFSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYESLIKFSNISFH 253
            N      V      + +E +  E    +        +S   LE+LK +SL  F+ +   
Sbjct: 190 PNAEVEEEVPFAEPVDPDEVLDEEEEEEEAEEEDAEAISNANLEELKLQSLEHFALVRAL 249

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           F+++     K+G  SE Y +    I+   + +RF  + IE LC++LR+++N++   E+ I
Sbjct: 250 FEELVVVLRKQGNQSEEYRQLQGAITESFMKVRFATRQIESLCESLRSRVNEIRSYERDI 309

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I V +  M R HFIK FP NEIN +WV++E      ++  L R   +I E Q KL  L
Sbjct: 310 QDICVTRVRMDRAHFIKYFPGNEINTDWVEDEISSGKPWSEALTRFKYAIIEKQTKLAEL 369

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           Q   +L + DL++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 370 QDRAMLSIKDLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 429

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 430 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 489

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQILQETG EPDP+ +A +MEMPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+N
Sbjct: 490 RQILQETGHEPDPAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQN 549

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            LAPSDAA+ +S++   K++L +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 550 NLAPSDAAMYSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 609

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 610 RQIEAKALRKLR 621


>gi|224823888|ref|ZP_03696997.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudogulbenkiania
            ferrooxidans 2002]
 gi|224604343|gb|EEG10517.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudogulbenkiania
            ferrooxidans 2002]
          Length = 640

 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/625 (58%), Positives = 467/625 (74%), Gaps = 13/625 (2%)

Query: 817  DIKSNSREE--IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 874
            D++ N +E   +E+ RK+ ++LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10   DMQDNEQESMSLEDQRKRLRLLIALGKERGYLTYAEINDHLPEDVSDTEQIENIVTMITG 69

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 931
            + I V +   D +TL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70   LGIQVYDEAPDADTLLMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 932  VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 991
            VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   +++   +I++DE+VDG ID
Sbjct: 130  VELLTREGEIEIAKRIEDGLKHMIEAISACPGTISEVLALLERVEAGDIRVDEVVDGFID 189

Query: 992  KNFSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYESLIKFSNISFH 1043
             N      V      + +E +  E    +        +S   LE+LK +SL  F+ +   
Sbjct: 190  PNAEVEEEVPFAEPVDPDEVLDEEEEEEEAEEEDAEAISNANLEELKLQSLEHFALVRAL 249

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            F+++     K+G  SE Y +    I+   + +RF  + IE LC++LR+++N++   E+ I
Sbjct: 250  FEELVVVLRKQGNQSEEYRQLQGAITESFMKVRFATRQIESLCESLRSRVNEIRSYERDI 309

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I V +  M R HFIK FP NEIN +WV++E      ++  L R   +I E Q KL  L
Sbjct: 310  QDICVTRVRMDRAHFIKYFPGNEINTDWVEDEISSGKPWSEALTRFKYAIIEKQTKLAEL 369

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            Q   +L + DL++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 370  QDRAMLSIKDLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 429

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 430  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 489

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQILQETG EPDP+ +A +MEMPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+N
Sbjct: 490  RQILQETGHEPDPAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQN 549

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             LAPSDAA+ +S++   K++L +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 550  NLAPSDAAMYSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 609

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHP+R  +L+ FL+
Sbjct: 610  RQIEAKALRKLRHPTRSERLRSFLD 634



 Score =  701 bits (1809), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/612 (58%), Positives = 457/612 (74%), Gaps = 13/612 (2%)

Query: 27  DIKSNSREE--IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY 84
           D++ N +E   +E+ RK+ ++LI LGKERGYLT++EIND LPED+ D E IE+I+     
Sbjct: 10  DMQDNEQESMSLEDQRKRLRLLIALGKERGYLTYAEINDHLPEDVSDTEQIENIVTMITG 69

Query: 85  MDISVSEHVLDTETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGS 141
           + I V +   D +TL++S+ T     E+A E A   LS+VDS+FGRT DP++MYMREMGS
Sbjct: 70  LGIQVYDEAPDADTLLMSDATPAVADEDAVEEAEAALSSVDSEFGRTTDPVRMYMREMGS 129

Query: 142 VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 201
           VELLTR+GEIEIAKRIE+GLK MI AIS+CP TI E+L   +++   +I++DE+VDG ID
Sbjct: 130 VELLTREGEIEIAKRIEDGLKHMIEAISACPGTISEVLALLERVEAGDIRVDEVVDGFID 189

Query: 202 KNFSSNNRVIKGNKNNNEEKILIESSSAD--------LSTEQLEKLKYESLIKFSNISFH 253
            N      V      + +E +  E    +        +S   LE+LK +SL  F+ +   
Sbjct: 190 PNAEVEEEVPFAEPVDPDEVLDEEEEEEEAEEEDAEAISNANLEELKLQSLEHFALVRAL 249

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           F+++     K+G  SE Y +    I+   + +RF  + IE LC++LR+++N++   E+ I
Sbjct: 250 FEELVVVLRKQGNQSEEYRQLQGAITESFMKVRFATRQIESLCESLRSRVNEIRSYERDI 309

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I V +  M R HFIK FP NEIN +WV++E      ++  L R   +I E Q KL  L
Sbjct: 310 QDICVTRVRMDRAHFIKYFPGNEINTDWVEDEISSGKPWSEALTRFKYAIIEKQTKLAEL 369

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           Q   +L + DL++INR+M AGE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 370 QDRAMLSIKDLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQE 429

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 430 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 489

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQILQETG EPDP+ +A +MEMPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED+N
Sbjct: 490 RQILQETGHEPDPAELAERMEMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQN 549

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            LAPSDAA+ +S++   K++L +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 550 NLAPSDAAMYSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 609

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 610 RQIEAKALRKLR 621


>gi|226939395|ref|YP_002794468.1| RNA polymerase sigma factor RpoD [Laribacter hongkongensis HLHK9]
 gi|226714321|gb|ACO73459.1| RpoD [Laribacter hongkongensis HLHK9]
          Length = 649

 Score =  713 bits (1841), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/621 (57%), Positives = 461/621 (74%), Gaps = 18/621 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  RK+ K LI  GKERG+LT++EIND LPED++D E IESII     M I V +   D 
Sbjct: 24   EERRKRLKQLIVQGKERGFLTYAEINDSLPEDVLDAEQIESIIGMITDMGIQVYDEAPDA 83

Query: 887  ETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            E L++S+ T   +D+D  E  E+ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEI
Sbjct: 84   EQLLMSDATPVVADEDAVEEAESALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 143

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------- 993
            AKRIE+GL+ M+ AIS+CP  + ++L   +K+  +E++IDE++DG+ID N          
Sbjct: 144  AKRIEDGLRHMVQAISACPGIVKDVLDQIEKVENDELRIDEVIDGIIDPNAPDEADARAE 203

Query: 994  -----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
                  +  +       ++ EE+   E  +       LE+LK ++L  F+N+   ++KM 
Sbjct: 204  AELAAVNEQDAEADEADDDGEEEENAEEGTPAAPGTNLEELKAQALEHFANVRKLYEKMV 263

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
            KA  K G  S+ Y++    I+   L +RF+A+ +E L D LR+ ++ + + E++I +I V
Sbjct: 264  KALVKHGPQSKQYLEVQAEITETFLLVRFSARQVEALSDRLRSVVDDIRRNEREIQDICV 323

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
             KC MPR  F+  F  NE NL WVD    +   +   + R   +I+E Q  LI LQ   +
Sbjct: 324  QKCKMPRDVFLHTFVNNETNLEWVDAAMSLGKAFASAIERYQHAIREKQSNLIALQDSSM 383

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            LP+ +L++I+R+M  GE KARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 384  LPIRELKEISRQMATGEAKARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 443

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 444  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 503

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG+EPDP+ +A +M+MPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   +APS
Sbjct: 504  ETGAEPDPAELARRMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDLATMAPS 563

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA+ AS++   K++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 564  DAAMYASLKEATKEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 623

Query: 1409 KALRKLRHPSRYYKLKIFLEG 1429
            KALRKLRHP+R  +L+ FL+ 
Sbjct: 624  KALRKLRHPTRSERLRSFLDA 644



 Score =  697 bits (1800), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 351/607 (57%), Positives = 451/607 (74%), Gaps = 18/607 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  RK+ K LI  GKERG+LT++EIND LPED++D E IESII     M I V +   D 
Sbjct: 24  EERRKRLKQLIVQGKERGFLTYAEINDSLPEDVLDAEQIESIIGMITDMGIQVYDEAPDA 83

Query: 97  ETLMLSNIT---SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           E L++S+ T   +D+D  E  E+ALS+VDS+FGRT DP++MYMREMG+VELLTR+GEIEI
Sbjct: 84  EQLLMSDATPVVADEDAVEEAESALSSVDSEFGRTTDPVRMYMREMGTVELLTREGEIEI 143

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------- 203
           AKRIE+GL+ M+ AIS+CP  + ++L   +K+  +E++IDE++DG+ID N          
Sbjct: 144 AKRIEDGLRHMVQAISACPGIVKDVLDQIEKVENDELRIDEVIDGIIDPNAPDEADARAE 203

Query: 204 -----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
                 +  +       ++ EE+   E  +       LE+LK ++L  F+N+   ++KM 
Sbjct: 204 AELAAVNEQDAEADEADDDGEEEENAEEGTPAAPGTNLEELKAQALEHFANVRKLYEKMV 263

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
           KA  K G  S+ Y++    I+   L +RF+A+ +E L D LR+ ++ + + E++I +I V
Sbjct: 264 KALVKHGPQSKQYLEVQAEITETFLLVRFSARQVEALSDRLRSVVDDIRRNEREIQDICV 323

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
            KC MPR  F+  F  NE NL WVD    +   +   + R   +I+E Q  LI LQ   +
Sbjct: 324 QKCKMPRDVFLHTFVNNETNLEWVDAAMSLGKAFASAIERYQHAIREKQSNLIALQDSSM 383

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           LP+ +L++I+R+M  GE KARKAKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 384 LPIRELKEISRQMATGEAKARKAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 443

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 444 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 503

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG+EPDP+ +A +M+MPE+KIRKIMKI+KEP+SME+P+GDD+DSHLGDFIED   +APS
Sbjct: 504 ETGAEPDPAELARRMDMPEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDLATMAPS 563

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA+ AS++   K++L+SLTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 564 DAAMYASLKEATKEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 623

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 624 KALRKLR 630


>gi|91776674|ref|YP_546430.1| sigma 70 (RpoD) [Methylobacillus flagellatus KT]
 gi|91710661|gb|ABE50589.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacillus flagellatus
            KT]
          Length = 644

 Score =  712 bits (1838), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/612 (58%), Positives = 453/612 (74%), Gaps = 13/612 (2%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            R + K LI LGKERGYLT++EIND LP+D+ D E I+SII     M I V E   D E L
Sbjct: 29   RTRLKSLIILGKERGYLTYAEINDHLPDDVQDSEQIDSIIGMINDMGIQVYEEAPDAEAL 88

Query: 890  MLSNI---TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            ++S++    +D+D  E  E ALSTVDS+FGRT DP++MYMREMG+V+LLTR+GEIEIAKR
Sbjct: 89   LMSDVPAPVADEDAVEEAEQALSTVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKR 148

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+GLK M+ AI++CP+TI E+L   D++ K E+ +D++VDGLID +      ++     
Sbjct: 149  IEDGLKHMVQAIAACPSTIAELLAMVDQVEKGELGVDDLVDGLIDADDGLGAEIVAEEAA 208

Query: 1007 NNEE----------KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            +  +          +    + +A +S E L +L+ E L +F+ I    +KM      +G 
Sbjct: 209  DAGDVAEDADEEDEEDDDGAKAAAISAEALARLREEVLTRFAVIRSAHEKMTVLLASKGS 268

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              + Y+K    I  E++  RF+AK +E LCD +R  + ++   E++I++  V K GMPR 
Sbjct: 269  QDKEYLKLQATIIEELMAFRFSAKQVEALCDRVRGMVEEIRSHERKIMDFCVEKAGMPRA 328

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            HFIK FP NE N  W+  E  +   Y   L R   SI + QQ+L+ +Q  + +P+ +L++
Sbjct: 329  HFIKSFPGNEGNPEWLAAELAVNKPYVERLERFRHSIDDQQQQLLAIQERVGIPIRELKE 388

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            IN++M  GE +AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 389  INKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 448

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP
Sbjct: 449  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDP 508

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
            + +A KMEMPE+KIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP DAA+ AS+
Sbjct: 509  ATLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDVATLAPVDAAVYASL 568

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R   K++L SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 569  RDATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 628

Query: 1417 PSRYYKLKIFLE 1428
            P+R  +L+ FLE
Sbjct: 629  PTRSERLRSFLE 640



 Score =  696 bits (1795), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/599 (58%), Positives = 443/599 (73%), Gaps = 13/599 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + K LI LGKERGYLT++EIND LP+D+ D E I+SII     M I V E   D E L
Sbjct: 29  RTRLKSLIILGKERGYLTYAEINDHLPDDVQDSEQIDSIIGMINDMGIQVYEEAPDAEAL 88

Query: 100 MLSNI---TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           ++S++    +D+D  E  E ALSTVDS+FGRT DP++MYMREMG+V+LLTR+GEIEIAKR
Sbjct: 89  LMSDVPAPVADEDAVEEAEQALSTVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKR 148

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+GLK M+ AI++CP+TI E+L   D++ K E+ +D++VDGLID +      ++     
Sbjct: 149 IEDGLKHMVQAIAACPSTIAELLAMVDQVEKGELGVDDLVDGLIDADDGLGAEIVAEEAA 208

Query: 217 NNEE----------KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           +  +          +    + +A +S E L +L+ E L +F+ I    +KM      +G 
Sbjct: 209 DAGDVAEDADEEDEEDDDGAKAAAISAEALARLREEVLTRFAVIRSAHEKMTVLLASKGS 268

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             + Y+K    I  E++  RF+AK +E LCD +R  + ++   E++I++  V K GMPR 
Sbjct: 269 QDKEYLKLQATIIEELMAFRFSAKQVEALCDRVRGMVEEIRSHERKIMDFCVEKAGMPRA 328

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           HFIK FP NE N  W+  E  +   Y   L R   SI + QQ+L+ +Q  + +P+ +L++
Sbjct: 329 HFIKSFPGNEGNPEWLAAELAVNKPYVERLERFRHSIDDQQQQLLAIQERVGIPIRELKE 388

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           IN++M  GE +AR+AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 389 INKQMSTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 448

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP
Sbjct: 449 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDP 508

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
           + +A KMEMPE+KIRKI+KI+KEP+SME+P+GDD+DSHLGDFIED   LAP DAA+ AS+
Sbjct: 509 ATLAEKMEMPEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDVATLAPVDAAVYASL 568

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R   K++L SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 569 RDATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 627


>gi|253997427|ref|YP_003049491.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera mobilis JLW8]
 gi|253984106|gb|ACT48964.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera mobilis JLW8]
          Length = 646

 Score =  707 bits (1826), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/638 (56%), Positives = 469/638 (73%), Gaps = 16/638 (2%)

Query: 809  SKKNAFSFDIKSNSREEI--ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIE 866
            ++KNA  + + +   +E+  E  R + K LI LGKERGYLT++EIND LP+D+   E I+
Sbjct: 11   AEKNAEDY-VHTEQLQEVSAEERRIRLKSLIVLGKERGYLTYAEINDHLPDDVQGSEQID 69

Query: 867  SIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPI 922
             II     M I V E   D E L++S+    +T DD VEEA E AL+TVDS+FGRT DP+
Sbjct: 70   GIIGMINDMGIQVYEETPDAEALLMSDAPPAVTDDDAVEEA-EQALATVDSEFGRTTDPV 128

Query: 923  KMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKI 982
            +MYMREMG+V+LLTR+ EIEIA+RIE+GLK M+ AI++CPTTI  +L   DK+ ++E+ +
Sbjct: 129  RMYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLEMVDKVERDELSV 188

Query: 983  DEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLS--------TEQLEKLKYESL 1034
            D++VDGLID +   ++ + +  +++ E ++  +    D           E L KLK E L
Sbjct: 189  DDLVDGLIDSDIGLDDAMTEDTQDDEEPEVDEDEDEGDEDGAKAAAISAEALAKLKEELL 248

Query: 1035 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 1094
             +F  +     KM      +G     Y+   + I  E+   RF+ K +E LCD +R  + 
Sbjct: 249  KRFEVVRAAHQKMTVILPVKGSQDPVYLALLSEILVELTAFRFSPKQVETLCDQVRGLVE 308

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
             V   E+++L+  V K GMPR +FIK FP NE NL W+D+E K+ + YN  L R   SI 
Sbjct: 309  TVRGHERKVLDFCVEKAGMPRPYFIKSFPGNESNLAWLDDELKLDNPYNEKLARFNHSIL 368

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
            + QQ++I+L+T + +   +L++IN++M  GE +AR+AKREM EANLRLVISIAKKYT+RG
Sbjct: 369  DQQQRIIDLETKVGISAKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRG 428

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 429  LQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 488

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++RISRQILQETG EPDP+++A KMEMPE+KIRKI+KI+KEP+SME+P+GDDEDSH
Sbjct: 489  TINKMNRISRQILQETGIEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIGDDEDSH 548

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED   LAP DAA+ AS+R    ++L SLTPRE+KVLRMRFGIEM++DHTLEEVGK
Sbjct: 549  LGDFIEDSTTLAPVDAAVYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGK 608

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            QFDVTRERIRQIEAKALRKLRHP+R  +L+ FLE  ++
Sbjct: 609  QFDVTRERIRQIEAKALRKLRHPTRSERLRSFLETGQD 646



 Score =  692 bits (1787), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/629 (56%), Positives = 460/629 (73%), Gaps = 16/629 (2%)

Query: 11  KNKKTKETLLKNAFSFDIKSNSREEI--ENLRKKFKILIKLGKERGYLTFSEINDFLPED 68
           + KK+ +   KNA  + + +   +E+  E  R + K LI LGKERGYLT++EIND LP+D
Sbjct: 3   RPKKSDQQAEKNAEDY-VHTEQLQEVSAEERRIRLKSLIVLGKERGYLTYAEINDHLPDD 61

Query: 69  IIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSD 124
           +   E I+ II     M I V E   D E L++S+    +T DD VEEA E AL+TVDS+
Sbjct: 62  VQGSEQIDGIIGMINDMGIQVYEETPDAEALLMSDAPPAVTDDDAVEEA-EQALATVDSE 120

Query: 125 FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADK 184
           FGRT DP++MYMREMG+V+LLTR+ EIEIA+RIE+GLK M+ AI++CPTTI  +L   DK
Sbjct: 121 FGRTTDPVRMYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLEMVDK 180

Query: 185 ISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLS--------TEQL 236
           + ++E+ +D++VDGLID +   ++ + +  +++ E ++  +    D           E L
Sbjct: 181 VERDELSVDDLVDGLIDSDIGLDDAMTEDTQDDEEPEVDEDEDEGDEDGAKAAAISAEAL 240

Query: 237 EKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLC 296
            KLK E L +F  +     KM      +G     Y+   + I  E+   RF+ K +E LC
Sbjct: 241 AKLKEELLKRFEVVRAAHQKMTVILPVKGSQDPVYLALLSEILVELTAFRFSPKQVETLC 300

Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 356
           D +R  +  V   E+++L+  V K GMPR +FIK FP NE NL W+D+E K+ + YN  L
Sbjct: 301 DQVRGLVETVRGHERKVLDFCVEKAGMPRPYFIKSFPGNESNLAWLDDELKLDNPYNEKL 360

Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
            R   SI + QQ++I+L+T + +   +L++IN++M  GE +AR+AKREM EANLRLVISI
Sbjct: 361 ARFNHSILDQQQRIIDLETKVGISAKELKEINKQMTTGEARARRAKREMIEANLRLVISI 420

Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
           AKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTI
Sbjct: 421 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTI 480

Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536
           RIPVHMIETINK++RISRQILQETG EPDP+++A KMEMPE+KIRKI+KI+KEP+SME+P
Sbjct: 481 RIPVHMIETINKMNRISRQILQETGIEPDPALLAEKMEMPEDKIRKILKISKEPISMETP 540

Query: 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596
           +GDDEDSHLGDFIED   LAP DAA+ AS+R    ++L SLTPRE+KVLRMRFGIEM++D
Sbjct: 541 IGDDEDSHLGDFIEDSTTLAPVDAAVYASLRDATSEVLESLTPREAKVLRMRFGIEMNTD 600

Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           HTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 601 HTLEEVGKQFDVTRERIRQIEAKALRKLR 629


>gi|297539657|ref|YP_003675426.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera versatilis 301]
 gi|297259004|gb|ADI30849.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera versatilis 301]
          Length = 645

 Score =  707 bits (1825), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/633 (57%), Positives = 463/633 (73%), Gaps = 13/633 (2%)

Query: 808  FSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIES 867
             ++KN   F          E  R + K LI LGKERGYLT++EIND LP+D+ + E I+ 
Sbjct: 10   LAEKNKMEFVSPELQEASAEERRSRLKSLIVLGKERGYLTYAEINDHLPDDVQNSEQIDG 69

Query: 868  IIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIK 923
            II     M I V E   D E L++S+    +T +D VEEA E AL+TVDSDFGRT DP++
Sbjct: 70   IIGMINDMGIQVYEEAPDAEVLLMSDAPPAVTDEDAVEEA-EQALATVDSDFGRTTDPVR 128

Query: 924  MYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKID 983
            MYMREMG+V+LLTR+ EIEIA+RIE+GLK M+ AI++CPTTI  +L   DK+  +E+ +D
Sbjct: 129  MYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLALVDKVENDELSVD 188

Query: 984  EIVDGLIDKNFSSNNRVI--------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 1035
            ++VDGLID +  +   V+        + +++ +E +    + +A +S E L KLK E + 
Sbjct: 189  DLVDGLIDSDVGAVADVVIEAAEDEDEVDEDIDEGEDEDGAKAAAISAEALAKLKEEVVN 248

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            +F+ +     KM +     G     Y    + I  E+   RF+ K +E LCD +R+ +  
Sbjct: 249  RFTVVRAANKKMTEILPLRGSQDPQYQALLSEILVELTAFRFSPKQVEGLCDQVRDLVET 308

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            +   E+++L+  V K GMPRLHFIK FP NE NL W+  E K    Y   L R   SI +
Sbjct: 309  IRSHERKVLDFCVEKSGMPRLHFIKSFPGNESNLGWLAEELKADKPYIEKLIRYNHSILD 368

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
             QQ+LI+L+ ++ +P+ +L++IN++M  GE +AR+AKREM EANLRLVISIAKKYT+RGL
Sbjct: 369  QQQRLIDLEKNVGIPIKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRGL 428

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 429  QFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 488

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQILQETG EPDP+++A KMEMPE+KIRKI+KI+KEP+SME+P+GDDEDSHL
Sbjct: 489  INKMNRISRQILQETGVEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIGDDEDSHL 548

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED   LAP DAA+ AS+R    ++L SLTPRE+KVLRMRFGIEM++DHTLEEVGKQ
Sbjct: 549  GDFIEDGQTLAPVDAAIYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQ 608

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            FDVTRERIRQIEAKALRKLRHP+R  +L+ FLE
Sbjct: 609  FDVTRERIRQIEAKALRKLRHPTRSERLRSFLE 641



 Score =  691 bits (1784), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/627 (57%), Positives = 456/627 (72%), Gaps = 13/627 (2%)

Query: 11  KNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDII 70
           + KK+ +   KN   F          E  R + K LI LGKERGYLT++EIND LP+D+ 
Sbjct: 3   RPKKSDQLAEKNKMEFVSPELQEASAEERRSRLKSLIVLGKERGYLTYAEINDHLPDDVQ 62

Query: 71  DHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFG 126
           + E I+ II     M I V E   D E L++S+    +T +D VEEA E AL+TVDSDFG
Sbjct: 63  NSEQIDGIIGMINDMGIQVYEEAPDAEVLLMSDAPPAVTDEDAVEEA-EQALATVDSDFG 121

Query: 127 RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKIS 186
           RT DP++MYMREMG+V+LLTR+ EIEIA+RIE+GLK M+ AI++CPTTI  +L   DK+ 
Sbjct: 122 RTTDPVRMYMREMGTVDLLTRESEIEIARRIEDGLKHMVQAIAACPTTIAALLALVDKVE 181

Query: 187 KNEIKIDEIVDGLIDKNFSSNNRVI--------KGNKNNNEEKILIESSSADLSTEQLEK 238
            +E+ +D++VDGLID +  +   V+        + +++ +E +    + +A +S E L K
Sbjct: 182 NDELSVDDLVDGLIDSDVGAVADVVIEAAEDEDEVDEDIDEGEDEDGAKAAAISAEALAK 241

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK E + +F+ +     KM +     G     Y    + I  E+   RF+ K +E LCD 
Sbjct: 242 LKEEVVNRFTVVRAANKKMTEILPLRGSQDPQYQALLSEILVELTAFRFSPKQVEGLCDQ 301

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           +R+ +  +   E+++L+  V K GMPRLHFIK FP NE NL W+  E K    Y   L R
Sbjct: 302 VRDLVETIRSHERKVLDFCVEKSGMPRLHFIKSFPGNESNLGWLAEELKADKPYIEKLIR 361

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
              SI + QQ+LI+L+ ++ +P+ +L++IN++M  GE +AR+AKREM EANLRLVISIAK
Sbjct: 362 YNHSILDQQQRLIDLEKNVGIPIKELKEINKQMTTGEARARRAKREMIEANLRLVISIAK 421

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 422 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRI 481

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQILQETG EPDP+++A KMEMPE+KIRKI+KI+KEP+SME+P+G
Sbjct: 482 PVHMIETINKMNRISRQILQETGVEPDPALLAEKMEMPEDKIRKILKISKEPISMETPIG 541

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DDEDSHLGDFIED   LAP DAA+ AS+R    ++L SLTPRE+KVLRMRFGIEM++DHT
Sbjct: 542 DDEDSHLGDFIEDGQTLAPVDAAIYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHT 601

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR 625
           LEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 602 LEEVGKQFDVTRERIRQIEAKALRKLR 628


>gi|167584375|ref|ZP_02376763.1| sigma 70 (RpoD) [Burkholderia ubonensis Bu]
          Length = 611

 Score =  688 bits (1775), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 330/624 (52%), Positives = 449/624 (71%), Gaps = 42/624 (6%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             + LI LG+ERGYLT ++IND LP++      +E+I+ TF  M ++V E   D ETL+L+
Sbjct: 1    MRALIALGRERGYLTHADINDHLPDNFAQTAAMETIVSTFSDMGVAVYEQAPDAETLLLN 60

Query: 893  NIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            + T    SDD  +E  EAALSTVDS+FGRT DP++MYMREMG+ ELLTR GEIEIAKRIE
Sbjct: 61   DATAAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIEIAKRIE 120

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
             GL+DMI AI++CPT +  IL  AD+I+  E++IDE+VDG+ D              + +
Sbjct: 121  SGLQDMIQAIAACPTVVSTILADADRIAAGELRIDELVDGISD--------------DTD 166

Query: 1009 EEKILIESSSADL------------------------STEQLEKLKYESLIKFSNISFHF 1044
            E  + +ES   ++                        +T +LE+L  +SL  F+ +   F
Sbjct: 167  ESDMTLESDEVEVEADASDDDPDGDDDEADAGDSEKANTARLEELTNDSLAIFARVRALF 226

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +++      +   S + ++    I  E+  IRFTAK+I++LC ++ +Q+ +V  IE+ IL
Sbjct: 227  EQLPDVPATDKTRSAAAVQVRAEIQRELAPIRFTAKTIDRLCASVHDQVTEVRAIERSIL 286

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            EI V++CGMPR  F++ FP +E +L W          +   L R++P+I+  QQKLI+++
Sbjct: 287  EIAVDRCGMPRDAFVESFPGHETDLEWTSRTAATSKQFGAALERHLPAIQAGQQKLIDIE 346

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
            + ++LPL  L+ INR+M A E K R+AKR+M EANLRLVISIAKKY +RG+QFLDLIQEG
Sbjct: 347  SRVLLPLQQLKQINRQMSAAESKMRQAKRQMIEANLRLVISIAKKYVNRGMQFLDLIQEG 406

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHMIETINK++RISR
Sbjct: 407  NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMIETINKLNRISR 466

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            +ILQ+TG E  P+V+A +MEM EEK+R I+KIAK+PVS+E+PVGDD D+ LGD IED + 
Sbjct: 467  EILQQTGQEAHPAVLAKRMEMSEEKVRSILKIAKQPVSLETPVGDDADATLGDMIEDVSA 526

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
             +P++AA++A+MR+ + + L+ L+PRE+KVLRMRFG++ +SDHTLEEVGKQFDVTRERIR
Sbjct: 527  SSPAEAAIHANMRAAIDEALDGLSPREAKVLRMRFGLDTTSDHTLEEVGKQFDVTRERIR 586

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIE+KA+RKL HPSR  KL+ FLE
Sbjct: 587  QIESKAMRKLMHPSRADKLRPFLE 610



 Score =  670 bits (1729), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/610 (52%), Positives = 439/610 (71%), Gaps = 42/610 (6%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            + LI LG+ERGYLT ++IND LP++      +E+I+ TF  M ++V E   D ETL+L+
Sbjct: 1   MRALIALGRERGYLTHADINDHLPDNFAQTAAMETIVSTFSDMGVAVYEQAPDAETLLLN 60

Query: 103 NIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           + T    SDD  +E  EAALSTVDS+FGRT DP++MYMREMG+ ELLTR GEIEIAKRIE
Sbjct: 61  DATAAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIEIAKRIE 120

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
            GL+DMI AI++CPT +  IL  AD+I+  E++IDE+VDG+ D              + +
Sbjct: 121 SGLQDMIQAIAACPTVVSTILADADRIAAGELRIDELVDGISD--------------DTD 166

Query: 219 EEKILIESSSADL------------------------STEQLEKLKYESLIKFSNISFHF 254
           E  + +ES   ++                        +T +LE+L  +SL  F+ +   F
Sbjct: 167 ESDMTLESDEVEVEADASDDDPDGDDDEADAGDSEKANTARLEELTNDSLAIFARVRALF 226

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +++      +   S + ++    I  E+  IRFTAK+I++LC ++ +Q+ +V  IE+ IL
Sbjct: 227 EQLPDVPATDKTRSAAAVQVRAEIQRELAPIRFTAKTIDRLCASVHDQVTEVRAIERSIL 286

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           EI V++CGMPR  F++ FP +E +L W          +   L R++P+I+  QQKLI+++
Sbjct: 287 EIAVDRCGMPRDAFVESFPGHETDLEWTSRTAATSKQFGAALERHLPAIQAGQQKLIDIE 346

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
           + ++LPL  L+ INR+M A E K R+AKR+M EANLRLVISIAKKY +RG+QFLDLIQEG
Sbjct: 347 SRVLLPLQQLKQINRQMSAAESKMRQAKRQMIEANLRLVISIAKKYVNRGMQFLDLIQEG 406

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHMIETINK++RISR
Sbjct: 407 NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMIETINKLNRISR 466

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           +ILQ+TG E  P+V+A +MEM EEK+R I+KIAK+PVS+E+PVGDD D+ LGD IED + 
Sbjct: 467 EILQQTGQEAHPAVLAKRMEMSEEKVRSILKIAKQPVSLETPVGDDADATLGDMIEDVSA 526

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
            +P++AA++A+MR+ + + L+ L+PRE+KVLRMRFG++ +SDHTLEEVGKQFDVTRERIR
Sbjct: 527 SSPAEAAIHANMRAAIDEALDGLSPREAKVLRMRFGLDTTSDHTLEEVGKQFDVTRERIR 586

Query: 615 QIEAKALRKL 624
           QIE+KA+RKL
Sbjct: 587 QIESKAMRKL 596


>gi|421897753|ref|ZP_16328120.1| rna polymerase sigma d (sigma-70) factor protein, partial
           [Ralstonia solanacearum MolK2]
 gi|206588959|emb|CAQ35921.1| rna polymerase sigma d (sigma-70) factor protein, partial
           [Ralstonia solanacearum MolK2]
          Length = 773

 Score =  685 bits (1767), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/557 (60%), Positives = 430/557 (77%), Gaps = 15/557 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 168 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 227

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 228 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 287

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 288 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 347

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADL 231
           ++++ +E KIDE +DGLID N  +  +                 +  E++    +  A  
Sbjct: 348 ERVANDEAKIDEYIDGLIDPNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAA 407

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           S  QLE+LK  +L KFS I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA++
Sbjct: 408 SARQLEELKQAALEKFSIIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARN 467

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++        
Sbjct: 468 VERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP 527

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ I+ RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLR
Sbjct: 528 YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLR 587

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 588 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 647

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPV 531
           QARTIRIPVHMIETINK++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+
Sbjct: 648 QARTIRIPVHMIETINKMNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPI 707

Query: 532 SMESPVGDDEDSHLGDF 548
           SM++P+GDD+DSHLGDF
Sbjct: 708 SMKTPIGDDDDSHLGDF 724



 Score =  677 bits (1746), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/540 (61%), Positives = 421/540 (77%), Gaps = 15/540 (2%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 185  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 244

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 245  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 304

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 305  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 364

Query: 990  IDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            ID N  +  +                 +  E++    +  A  S  QLE+LK  +L KFS
Sbjct: 365  IDPNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAASARQLEELKQAALEKFS 424

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V +
Sbjct: 425  IIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRK 484

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQ
Sbjct: 485  LERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQ 544

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFL
Sbjct: 545  KLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFL 604

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 605  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 664

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SM++P+GDD+DSHLGDF
Sbjct: 665  MNRISRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMKTPIGDDDDSHLGDF 724


>gi|295700891|ref|YP_003608784.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1002]
 gi|295440104|gb|ADG19273.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 665

 Score =  684 bits (1765), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 332/623 (53%), Positives = 451/623 (72%), Gaps = 22/623 (3%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            + E  ++  + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E   
Sbjct: 45   QAEERQRLMRALIQLGKEQGYLTHAQINDHLPDNFTATAAIDSIVSAFSDMGVQVYEQAP 104

Query: 885  DTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR GE
Sbjct: 105  DAETLLLNSNSPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGE 164

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            I IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL ++   +   V
Sbjct: 165  IAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGL-NEETGAAEEV 223

Query: 1001 IKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
               + +  E+ +                +SS+AD +  +L++L  + L  F+ +   +D+
Sbjct: 224  ESADADAEEDGVADEDSDDEEEDDDGPADSSAADEA--RLKQLTSDCLEIFAQVGILYDE 281

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M  A  +    S+ Y++A   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+I
Sbjct: 282  MNAAHTRGDVTSKGYLRAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQI 341

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYNLILCRNIPSIKELQQKLINLQT 1165
            VV+K GMPR  FI+ F  NE +L W +   +     Y   L R++P+I+  QQKLI+++ 
Sbjct: 342  VVSKAGMPREKFIETFAGNEADLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEA 401

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INRKM+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402  TVSLPLKHLKEINRKMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  P+V+A +ME+ EEK+R I+KIAK+PVS+E+PVGDD D+ LGD IED  + 
Sbjct: 522  ILQQTGQEAHPAVLAERMELSEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVS 581

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 642  IESKAMRKLMHPSRADRLKSFLD 664



 Score =  667 bits (1722), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/609 (53%), Positives = 441/609 (72%), Gaps = 22/609 (3%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           + E  ++  + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E   
Sbjct: 45  QAEERQRLMRALIQLGKEQGYLTHAQINDHLPDNFTATAAIDSIVSAFSDMGVQVYEQAP 104

Query: 95  DTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR GE
Sbjct: 105 DAETLLLNSNSPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGE 164

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           I IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL ++   +   V
Sbjct: 165 IAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGL-NEETGAAEEV 223

Query: 211 IKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
              + +  E+ +                +SS+AD +  +L++L  + L  F+ +   +D+
Sbjct: 224 ESADADAEEDGVADEDSDDEEEDDDGPADSSAADEA--RLKQLTSDCLEIFAQVGILYDE 281

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M  A  +    S+ Y++A   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+I
Sbjct: 282 MNAAHTRGDVTSKGYLRAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQI 341

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYNLILCRNIPSIKELQQKLINLQT 375
           VV+K GMPR  FI+ F  NE +L W +   +     Y   L R++P+I+  QQKLI+++ 
Sbjct: 342 VVSKAGMPREKFIETFAGNEADLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEA 401

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INRKM+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402 TVSLPLKHLKEINRKMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  P+V+A +ME+ EEK+R I+KIAK+PVS+E+PVGDD D+ LGD IED  + 
Sbjct: 522 ILQQTGQEAHPAVLAERMELSEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVS 581

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 642 IESKAMRKL 650


>gi|118594360|ref|ZP_01551707.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440138|gb|EAV46765.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 654

 Score =  683 bits (1762), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/622 (57%), Positives = 452/622 (72%), Gaps = 12/622 (1%)

Query: 821  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVS 880
            N+ EE EN R + K LI +GKERGYLT++EIND LP+++ + E +E II     M I V 
Sbjct: 32   NNPEEAENRRLQLKALIIMGKERGYLTYAEINDHLPDEVSESEQVEGIIGIINDMGIMVY 91

Query: 881  EHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
            E   D E+L++S+     +D++  E  E AL+TVDS+FGRT DP++MYMREMG+V+LLTR
Sbjct: 92   EQAPDAESLLMSDDRAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGTVDLLTR 151

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------ 991
            +GEIEIAKRIE+GL+ M+ AIS+CP  I +++  A+K+ K E+ ++E VDGLID      
Sbjct: 152  EGEIEIAKRIEDGLRHMVQAISACPGIIDDLMNMAEKVKKEELGVEEFVDGLIDMEAERE 211

Query: 992  --KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
              K  ++  +      + +++       ++ +S E L  L  E L +F  I     K+ +
Sbjct: 212  LAKVEAALAQTDDEESDEDDDDENDSGKASGMSAEDLAILTKEVLSRFGKIKRAHKKLSE 271

Query: 1050 AFEKEGY-NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
              E++ + + E Y K  + I  E++  RF++K +E LCD +R  + Q+   E+ ++E  V
Sbjct: 272  LREQKKWTDDEEYKKHQDIILKELINFRFSSKFVEVLCDKVRTFVKQIRGHERAVMEFCV 331

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
             +  MPR HFIK FP NE NL W+  E K    Y   L +   SI + Q KLI L+    
Sbjct: 332  EESKMPRSHFIKSFPGNETNLKWLKEEIKSDKKYVESLEKLKHSILDQQSKLIALEELAG 391

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            +P+ + ++INR M  GE +A++AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 392  IPIKNFKEINRHMTTGEARAKRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 451

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 452  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQ 511

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
             TG EP+PS +A KMEMPEEKIRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   L P 
Sbjct: 512  STGQEPEPSELAEKMEMPEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVGTLTPD 571

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA+  S+RSV  +IL  LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 572  DAAVYGSLRSVTSEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 631

Query: 1409 KALRKLRHPSRYYKLKIFLEGK 1430
            KALRKLRHP+R  +LK FLEGK
Sbjct: 632  KALRKLRHPTRSERLKSFLEGK 653



 Score =  665 bits (1717), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/635 (56%), Positives = 454/635 (71%), Gaps = 20/635 (3%)

Query: 5   NKKTK--IKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
           +KKTK   + KK K+  LK+A       N+ EE EN R + K LI +GKERGYLT++EIN
Sbjct: 10  DKKTKRVTRVKKLKDLYLKDAV------NNPEEAENRRLQLKALIIMGKERGYLTYAEIN 63

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALS 119
           D LP+++ + E +E II     M I V E   D E+L++S+     +D++  E  E AL+
Sbjct: 64  DHLPDEVSESEQVEGIIGIINDMGIMVYEQAPDAESLLMSDDRAPVTDEEAAEEAEQALA 123

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG+V+LLTR+GEIEIAKRIE+GL+ M+ AIS+CP  I +++
Sbjct: 124 TVDSEFGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEDGLRHMVQAISACPGIIDDLM 183

Query: 180 IAADKISKNEIKIDEIVDGLID--------KNFSSNNRVIKGNKNNNEEKILIESSSADL 231
             A+K+ K E+ ++E VDGLID        K  ++  +      + +++       ++ +
Sbjct: 184 NMAEKVKKEELGVEEFVDGLIDMEAERELAKVEAALAQTDDEESDEDDDDENDSGKASGM 243

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY-NSESYIKAHNNISNEMLGIRFTAK 290
           S E L  L  E L +F  I     K+ +  E++ + + E Y K  + I  E++  RF++K
Sbjct: 244 SAEDLAILTKEVLSRFGKIKRAHKKLSELREQKKWTDDEEYKKHQDIILKELINFRFSSK 303

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
            +E LCD +R  + Q+   E+ ++E  V +  MPR HFIK FP NE NL W+  E K   
Sbjct: 304 FVEVLCDKVRTFVKQIRGHERAVMEFCVEESKMPRSHFIKSFPGNETNLKWLKEEIKSDK 363

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            Y   L +   SI + Q KLI L+    +P+ + ++INR M  GE +A++AKREM EANL
Sbjct: 364 KYVESLEKLKHSILDQQSKLIALEELAGIPIKNFKEINRHMTTGEARAKRAKREMIEANL 423

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 424 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 483

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQILQ TG EP+PS +A KMEMPEEKIRKI+KI+KEP
Sbjct: 484 DQARTIRIPVHMIETINKMNRISRQILQSTGQEPEPSELAEKMEMPEEKIRKILKISKEP 543

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDDEDSHLGDFIED   L P DAA+  S+RSV  +IL  LTPRE+KVLRMRFG
Sbjct: 544 ISMETPIGDDEDSHLGDFIEDVGTLTPDDAAVYGSLRSVTSEILEGLTPREAKVLRMRFG 603

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 604 IEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 638


>gi|78060207|ref|YP_366782.1| sigma 70 (RpoD) [Burkholderia sp. 383]
 gi|77964757|gb|ABB06138.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. 383]
          Length = 677

 Score =  679 bits (1753), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 326/629 (51%), Positives = 452/629 (71%), Gaps = 21/629 (3%)

Query: 817  DIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMD 876
            DI S +R+  E  +++ + LI LG+ERGYLT ++IND LP++      +++I+ TF  M 
Sbjct: 52   DIASLARQN-EERQRQMRALIALGRERGYLTHADINDHLPDNFAQTAAMDTIVSTFSDMG 110

Query: 877  ISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSV 932
            ++V E   D E L+L+     + SDD  +E  EAALSTVDS+FGRT DP++MYMREMG+ 
Sbjct: 111  VAVYEQAPDAEALLLTEAAPAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGAS 170

Query: 933  ELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK 992
            ELLTR GEIE+AKRIE+GL+DMI AI++CP+ +  IL   D+I   E++IDE+VDG+   
Sbjct: 171  ELLTRAGEIEVAKRIEDGLQDMIQAIAACPSIVSTILADVDRIVAGELRIDELVDGI--- 227

Query: 993  NFSSNNRVIKGNKNNNEEKILIE-------------SSSADLSTEQLEKLKYESLIKFSN 1039
            +  ++   +       E ++L                 S  ++  +LE+L  +SL+ F+ 
Sbjct: 228  SVDTDESEMTPESQEEEAEVLAADDDSDEDDVETDAGDSEKVNAARLEELTNDSLVIFAR 287

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F+++          S +  +    I  E+  IRFTAK+I++LC+ +  Q+ +V  I
Sbjct: 288  VRALFEQLPDVPVTGEARSAAAAQVRAAIQRELAPIRFTAKTIDRLCEIVHGQVTEVRAI 347

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +L I V++CGMPR  F++ FP +E +L+W          +   L R+ P+I+  QQK
Sbjct: 348  ERSVLAIAVDRCGMPRDAFVESFPGHETDLDWTSRTAATSQQFGAALERHQPAIQAAQQK 407

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L+++++ + LPL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLD
Sbjct: 408  LVDIESRVSLPLQQLKQINRQMSAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLD 467

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHMIETINK+
Sbjct: 468  LIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMIETINKL 527

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISR+ILQ+TG E  P+V+A +MEM EEK+R I+KIAK+PVS+E+PVGDD D+ LGD I
Sbjct: 528  NRISREILQQTGQEAHPAVLAKRMEMSEEKVRSILKIAKQPVSLETPVGDDADATLGDMI 587

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED +  +P++AA++A+MR+ + + LN L+PRE+KVLRMRFG++ +SDHTLEEVGKQFDVT
Sbjct: 588  EDVSASSPAEAAIHANMRAAIDEALNGLSPREAKVLRMRFGLDTNSDHTLEEVGKQFDVT 647

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIE+KA+RKL HPSR  KL+ FLE
Sbjct: 648  RERIRQIESKAMRKLMHPSRADKLRPFLE 676



 Score =  661 bits (1706), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/615 (51%), Positives = 442/615 (71%), Gaps = 21/615 (3%)

Query: 27  DIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMD 86
           DI S +R+  E  +++ + LI LG+ERGYLT ++IND LP++      +++I+ TF  M 
Sbjct: 52  DIASLARQN-EERQRQMRALIALGRERGYLTHADINDHLPDNFAQTAAMDTIVSTFSDMG 110

Query: 87  ISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSV 142
           ++V E   D E L+L+     + SDD  +E  EAALSTVDS+FGRT DP++MYMREMG+ 
Sbjct: 111 VAVYEQAPDAEALLLTEAAPAVASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGAS 170

Query: 143 ELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK 202
           ELLTR GEIE+AKRIE+GL+DMI AI++CP+ +  IL   D+I   E++IDE+VDG+   
Sbjct: 171 ELLTRAGEIEVAKRIEDGLQDMIQAIAACPSIVSTILADVDRIVAGELRIDELVDGI--- 227

Query: 203 NFSSNNRVIKGNKNNNEEKILIE-------------SSSADLSTEQLEKLKYESLIKFSN 249
           +  ++   +       E ++L                 S  ++  +LE+L  +SL+ F+ 
Sbjct: 228 SVDTDESEMTPESQEEEAEVLAADDDSDEDDVETDAGDSEKVNAARLEELTNDSLVIFAR 287

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F+++          S +  +    I  E+  IRFTAK+I++LC+ +  Q+ +V  I
Sbjct: 288 VRALFEQLPDVPVTGEARSAAAAQVRAAIQRELAPIRFTAKTIDRLCEIVHGQVTEVRAI 347

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +L I V++CGMPR  F++ FP +E +L+W          +   L R+ P+I+  QQK
Sbjct: 348 ERSVLAIAVDRCGMPRDAFVESFPGHETDLDWTSRTAATSQQFGAALERHQPAIQAAQQK 407

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L+++++ + LPL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLD
Sbjct: 408 LVDIESRVSLPLQQLKQINRQMSAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLD 467

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHMIETINK+
Sbjct: 468 LIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMIETINKL 527

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISR+ILQ+TG E  P+V+A +MEM EEK+R I+KIAK+PVS+E+PVGDD D+ LGD I
Sbjct: 528 NRISREILQQTGQEAHPAVLAKRMEMSEEKVRSILKIAKQPVSLETPVGDDADATLGDMI 587

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED +  +P++AA++A+MR+ + + LN L+PRE+KVLRMRFG++ +SDHTLEEVGKQFDVT
Sbjct: 588 EDVSASSPAEAAIHANMRAAIDEALNGLSPREAKVLRMRFGLDTNSDHTLEEVGKQFDVT 647

Query: 610 RERIRQIEAKALRKL 624
           RERIRQIE+KA+RKL
Sbjct: 648 RERIRQIESKAMRKL 662


>gi|73541439|ref|YP_295959.1| sigma-70 factor [Ralstonia eutropha JMP134]
 gi|72118852|gb|AAZ61115.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia eutropha JMP134]
          Length = 653

 Score =  679 bits (1752), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 328/625 (52%), Positives = 458/625 (73%), Gaps = 16/625 (2%)

Query: 819  KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDIS 878
            +S S +E     ++ + LI+LG++RGYLT ++I+D L E+  D   +ESI+ TF  M + 
Sbjct: 26   ESMSPDEANARTQQLRALIQLGRQRGYLTHADISDHLQENFTDTAAMESIVTTFAEMGVK 85

Query: 879  VSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            + E   D ETL+LS+   + SDD  +E  E ALSTVDS+FGRT DP++MYMREM S  LL
Sbjct: 86   IFEQTPDAETLLLSDNAVVASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMSSATLL 145

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR  E+E+AKRIE+GL +M+HAIS+CP+TI  IL  + +++  E+ ID++VDGL D++ +
Sbjct: 146  TRKEEVELAKRIEDGLNNMVHAISACPSTIATILELSGRVASAEMGIDDLVDGLTDESGA 205

Query: 996  -------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISF 1042
                          +      + +N ++    E S+   +   L KL+ E L +F+ +S 
Sbjct: 206  DAPVTASADDSDDDSADTADEDDSNEDDDDAEEGSTQQSAEADLAKLRDECLKRFARVSE 265

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             F+ MR+ +   G  S  ++ A + + +E+  IRFTAK+IE+LC  +++ ++ V  +E+Q
Sbjct: 266  QFELMRQEYAANGSGSAGFVTARDTVRDELRTIRFTAKTIERLCADVQSMVDDVRVVERQ 325

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            +++++V++CGM R   I  FP NE NL+W  +       Y+  + R +P ++  QQKLI+
Sbjct: 326  VVQLLVDRCGMDREDVIARFPGNETNLSWGRDLAAASRPYSAAVARALPDLEAHQQKLID 385

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            +Q    LPL +L+ +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 386  IQARAALPLAELKAVNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGLQFLDLIQ 445

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+
Sbjct: 446  EGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRL 505

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SR+++Q+TG EPDP+V+A +M+MPEEK+R IMKIA+EPVSME+PVG+D D+ LGD I D 
Sbjct: 506  SRELMQQTGKEPDPAVLAERMDMPEEKVRAIMKIAREPVSMETPVGEDGDTSLGDMIADS 565

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
            +   P+DAAL AS+R VV+++L+ LTPRE+KVLRMRFGI+M++D+TLEEVGKQFDVTRER
Sbjct: 566  DTATPADAALQASLREVVREMLDELTPREAKVLRMRFGIDMATDYTLEEVGKQFDVTRER 625

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFL 1427
            IRQIE+KA+RKLRHPSR  +L  +L
Sbjct: 626  IRQIESKAMRKLRHPSRADQLITYL 650



 Score =  668 bits (1723), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/628 (51%), Positives = 454/628 (72%), Gaps = 16/628 (2%)

Query: 14  KTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE 73
           K +E  +        +S S +E     ++ + LI+LG++RGYLT ++I+D L E+  D  
Sbjct: 11  KAREAGIVKGLGGSTESMSPDEANARTQQLRALIQLGRQRGYLTHADISDHLQENFTDTA 70

Query: 74  IIESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKD 130
            +ESI+ TF  M + + E   D ETL+LS+   + SDD  +E  E ALSTVDS+FGRT D
Sbjct: 71  AMESIVTTFAEMGVKIFEQTPDAETLLLSDNAVVASDDQADEEAEVALSTVDSEFGRTTD 130

Query: 131 PIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEI 190
           P++MYMREM S  LLTR  E+E+AKRIE+GL +M+HAIS+CP+TI  IL  + +++  E+
Sbjct: 131 PVRMYMREMSSATLLTRKEEVELAKRIEDGLNNMVHAISACPSTIATILELSGRVASAEM 190

Query: 191 KIDEIVDGLIDKNFS-------------SNNRVIKGNKNNNEEKILIESSSADLSTEQLE 237
            ID++VDGL D++ +              +      + +N ++    E S+   +   L 
Sbjct: 191 GIDDLVDGLTDESGADAPVTASADDSDDDSADTADEDDSNEDDDDAEEGSTQQSAEADLA 250

Query: 238 KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 297
           KL+ E L +F+ +S  F+ MR+ +   G  S  ++ A + + +E+  IRFTAK+IE+LC 
Sbjct: 251 KLRDECLKRFARVSEQFELMRQEYAANGSGSAGFVTARDTVRDELRTIRFTAKTIERLCA 310

Query: 298 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILC 357
            +++ ++ V  +E+Q+++++V++CGM R   I  FP NE NL+W  +       Y+  + 
Sbjct: 311 DVQSMVDDVRVVERQVVQLLVDRCGMDREDVIARFPGNETNLSWGRDLAAASRPYSAAVA 370

Query: 358 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 417
           R +P ++  QQKLI++Q    LPL +L+ +NRKM+A E + R+AK EMT+ANLRLVISIA
Sbjct: 371 RALPDLEAHQQKLIDIQARAALPLAELKAVNRKMLAAERQMRQAKHEMTQANLRLVISIA 430

Query: 418 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 477
           KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR
Sbjct: 431 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIR 490

Query: 478 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537
           +PVHMIE INK++R+SR+++Q+TG EPDP+V+A +M+MPEEK+R IMKIA+EPVSME+PV
Sbjct: 491 VPVHMIEQINKLNRLSRELMQQTGKEPDPAVLAERMDMPEEKVRAIMKIAREPVSMETPV 550

Query: 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 597
           G+D D+ LGD I D +   P+DAAL AS+R VV+++L+ LTPRE+KVLRMRFGI+M++D+
Sbjct: 551 GEDGDTSLGDMIADSDTATPADAALQASLREVVREMLDELTPREAKVLRMRFGIDMATDY 610

Query: 598 TLEEVGKQFDVTRERIRQIEAKALRKLR 625
           TLEEVGKQFDVTRERIRQIE+KA+RKLR
Sbjct: 611 TLEEVGKQFDVTRERIRQIESKAMRKLR 638


>gi|339325765|ref|YP_004685458.1| DNA-directed RNA polymerase sigma-70 subunit RpoD [Cupriavidus
            necator N-1]
 gi|338165922|gb|AEI76977.1| DNA-directed RNA polymerase sigma-70 subunit RpoD [Cupriavidus
            necator N-1]
          Length = 656

 Score =  679 bits (1751), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 325/611 (53%), Positives = 450/611 (73%), Gaps = 14/611 (2%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 43   QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVSTFAEMGVKIYEQTPDAETLL 102

Query: 891  LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            LS+   + SDD  +E  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 103  LSDGPVVASDDQADEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 162

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SN 997
            EEGL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +          ++
Sbjct: 163  EEGLNNMVHAISACPFTIAAILELSAKVASNEISIDDLVDGLSDESIAEAAVAAAADETD 222

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            + V   ++  ++ +   +  S   S E+ L +L+ E L +F+ ++  F+ M +     G 
Sbjct: 223  DSVDSADEAEDDSEDSDDEGSTQQSNEKALAQLREECLKRFARVTAQFELMCQESAANGA 282

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S +++ A + +  E+  IRFTAK+IE+LC  ++  +++V  +E+Q+++++V +CGM R 
Sbjct: 283  GSAAFLAARDAVREELRTIRFTAKTIERLCANVQAMVDEVRTVERQVVQLLVERCGMERE 342

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
              I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L L DL+ 
Sbjct: 343  EVIARFPGNETNLAWGQELVAQSRPYSAAVARALPDLEAHQQKLIDIQARAALSLPDLKG 402

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+ FLDLIQEGNIGLMKAVDKFE
Sbjct: 403  VNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFE 462

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+TG EPDP
Sbjct: 463  YRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQTGKEPDP 522

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
            +V+A ++EM E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DAAL A +
Sbjct: 523  AVLAERLEMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADAALQAGL 582

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+VV+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA++KLRH
Sbjct: 583  RAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKKLRH 642

Query: 1417 PSRYYKLKIFL 1427
            PSR  +L  +L
Sbjct: 643  PSRADQLITYL 653



 Score =  665 bits (1717), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/599 (53%), Positives = 442/599 (73%), Gaps = 14/599 (2%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 43  QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVSTFAEMGVKIYEQTPDAETLL 102

Query: 101 LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           LS+   + SDD  +E  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 103 LSDGPVVASDDQADEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 162

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SN 207
           EEGL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +          ++
Sbjct: 163 EEGLNNMVHAISACPFTIAAILELSAKVASNEISIDDLVDGLSDESIAEAAVAAAADETD 222

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           + V   ++  ++ +   +  S   S E+ L +L+ E L +F+ ++  F+ M +     G 
Sbjct: 223 DSVDSADEAEDDSEDSDDEGSTQQSNEKALAQLREECLKRFARVTAQFELMCQESAANGA 282

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S +++ A + +  E+  IRFTAK+IE+LC  ++  +++V  +E+Q+++++V +CGM R 
Sbjct: 283 GSAAFLAARDAVREELRTIRFTAKTIERLCANVQAMVDEVRTVERQVVQLLVERCGMERE 342

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
             I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L L DL+ 
Sbjct: 343 EVIARFPGNETNLAWGQELVAQSRPYSAAVARALPDLEAHQQKLIDIQARAALSLPDLKG 402

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+ FLDLIQEGNIGLMKAVDKFE
Sbjct: 403 VNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFE 462

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+TG EPDP
Sbjct: 463 YRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQTGKEPDP 522

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
           +V+A ++EM E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DAAL A +
Sbjct: 523 AVLAERLEMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADAALQAGL 582

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+VV+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA++KLR
Sbjct: 583 RAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKKLR 641


>gi|302877609|ref|YP_003846173.1| RNA polymerase sigma-70 subunit RpoD [Gallionella capsiferriformans
            ES-2]
 gi|302580398|gb|ADL54409.1| RNA polymerase, sigma 70 subunit, RpoD [Gallionella capsiferriformans
            ES-2]
          Length = 655

 Score =  678 bits (1749), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/630 (57%), Positives = 456/630 (72%), Gaps = 23/630 (3%)

Query: 823  REEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH 882
            +++I+  R   K LI LGKERGYLT++EIND LP D+++ E IES+      M I V + 
Sbjct: 26   QQDIDARRTSLKALIVLGKERGYLTYAEINDHLP-DMLEVEQIESVASMINDMGIRVCDV 84

Query: 883  VLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
              D E L++++     +D+D  E  EAALSTVDS+FGRT DP++MYMREMG+V+LLTR+ 
Sbjct: 85   APDAEALIMTDSAPTAADEDAAEEAEAALSTVDSEFGRTTDPVRMYMREMGTVDLLTREK 144

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EIEIAKRIEEG ++MI AIS+CP TI EIL  A KI  +EI+++E++DG +D      + 
Sbjct: 145  EIEIAKRIEEGQRNMIQAISACPVTIAEILSLAAKIEIDEIRVNELIDGFVDIELEDESG 204

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLE-------------------KLKYESLIKFSNI 1040
            +   +    ++    ESS    S +  E                   +LK ++L +F+ I
Sbjct: 205  LTASDDQEQDDAEEEESSEESSSEDGDEEDEEAMAAASAAAAAADLAQLKADALARFAVI 264

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            +  F KM KA+EK GY S  Y      I+ E++  RFTAK ++ LC+T+R  + ++   E
Sbjct: 265  ADLFSKMGKAYEKYGYLSAQYNVHQAGITEELMAFRFTAKQVDALCNTMRGLVEEIRTNE 324

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + I +I V K  MPR HFIK F  +E++++W+  E K    Y+ +L R   +I E QQ L
Sbjct: 325  RGIQDICVTKSKMPRPHFIKSFVGHEVDMDWLAQEIKAAKPYSELLVRYQHAIVEKQQNL 384

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            IN+Q  + LP+ DL++INR+M  GE ++ +AKR+M EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 385  INMQKRVGLPITDLKEINRRMTNGEARSHRAKRDMIEANLRLVISIAKKYTNRGLQFLDL 444

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 445  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 504

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQILQETG E D + +A KMEM E+KI KI+KIAKEP+SME+PVGDD+DSHLGDFIE
Sbjct: 505  RISRQILQETGQEADAATLAEKMEMTEDKIHKILKIAKEPISMETPVGDDDDSHLGDFIE 564

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D N   P +AA+  S+RS   DIL+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTR
Sbjct: 565  DSNTTVPIEAAVYESLRSATSDILDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTR 624

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            ERIRQIEAKALRKLRHPSR  KLK FL+ +
Sbjct: 625  ERIRQIEAKALRKLRHPSRSEKLKSFLDSE 654



 Score =  660 bits (1703), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 351/615 (57%), Positives = 445/615 (72%), Gaps = 23/615 (3%)

Query: 33  REEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH 92
           +++I+  R   K LI LGKERGYLT++EIND LP D+++ E IES+      M I V + 
Sbjct: 26  QQDIDARRTSLKALIVLGKERGYLTYAEINDHLP-DMLEVEQIESVASMINDMGIRVCDV 84

Query: 93  VLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
             D E L++++     +D+D  E  EAALSTVDS+FGRT DP++MYMREMG+V+LLTR+ 
Sbjct: 85  APDAEALIMTDSAPTAADEDAAEEAEAALSTVDSEFGRTTDPVRMYMREMGTVDLLTREK 144

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EIEIAKRIEEG ++MI AIS+CP TI EIL  A KI  +EI+++E++DG +D      + 
Sbjct: 145 EIEIAKRIEEGQRNMIQAISACPVTIAEILSLAAKIEIDEIRVNELIDGFVDIELEDESG 204

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLE-------------------KLKYESLIKFSNI 250
           +   +    ++    ESS    S +  E                   +LK ++L +F+ I
Sbjct: 205 LTASDDQEQDDAEEEESSEESSSEDGDEEDEEAMAAASAAAAAADLAQLKADALARFAVI 264

Query: 251 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
           +  F KM KA+EK GY S  Y      I+ E++  RFTAK ++ LC+T+R  + ++   E
Sbjct: 265 ADLFSKMGKAYEKYGYLSAQYNVHQAGITEELMAFRFTAKQVDALCNTMRGLVEEIRTNE 324

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           + I +I V K  MPR HFIK F  +E++++W+  E K    Y+ +L R   +I E QQ L
Sbjct: 325 RGIQDICVTKSKMPRPHFIKSFVGHEVDMDWLAQEIKAAKPYSELLVRYQHAIVEKQQNL 384

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
           IN+Q  + LP+ DL++INR+M  GE ++ +AKR+M EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 385 INMQKRVGLPITDLKEINRRMTNGEARSHRAKRDMIEANLRLVISIAKKYTNRGLQFLDL 444

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 445 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN 504

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQILQETG E D + +A KMEM E+KI KI+KIAKEP+SME+PVGDD+DSHLGDFIE
Sbjct: 505 RISRQILQETGQEADAATLAEKMEMTEDKIHKILKIAKEPISMETPVGDDDDSHLGDFIE 564

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D N   P +AA+  S+RS   DIL+SLT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTR
Sbjct: 565 DSNTTVPIEAAVYESLRSATSDILDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTR 624

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 625 ERIRQIEAKALRKLR 639


>gi|113867637|ref|YP_726126.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia eutropha
            H16]
 gi|113526413|emb|CAJ92758.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Ralstonia eutropha
            H16]
          Length = 656

 Score =  676 bits (1745), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/611 (53%), Positives = 451/611 (73%), Gaps = 14/611 (2%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 43   QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVSTFAEMGVKIYEQTPDAETLL 102

Query: 891  LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            LS+   + SDD  +E  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 103  LSDGPVVASDDQADEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 162

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SN 997
            EEGL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +          ++
Sbjct: 163  EEGLNNMVHAISACPFTIAAILELSGKVASNEISIDDLVDGLSDESIAEAAVAAAADETD 222

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            + V   ++ +++ +   +  S   S E+ L +L+ E L +F+ ++  F+ M +     G 
Sbjct: 223  DSVDSADEADDDSEDSDDEGSTQQSNEKALAQLREECLKRFARVTAQFELMCQESAANGA 282

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S +++ A + +  E+  IRFTAK+IE+LC  ++  +++V  +E+Q+++++V +CGM R 
Sbjct: 283  GSAAFLAARDAVREELRTIRFTAKTIERLCANVQAMVDEVRTVERQVVQLLVERCGMERE 342

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
              I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L L DL+ 
Sbjct: 343  EVIARFPGNETNLAWGQELVAQSRPYSAAVARALPDLEAHQQKLIDIQARAALSLPDLKG 402

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+ FLDLIQEGNIGLMKAVDKFE
Sbjct: 403  VNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFE 462

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+TG EPDP
Sbjct: 463  YRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQTGKEPDP 522

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
            +V+A +++M E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DAAL A +
Sbjct: 523  AVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADAALQAGL 582

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+VV+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA++KLRH
Sbjct: 583  RAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKKLRH 642

Query: 1417 PSRYYKLKIFL 1427
            PSR  +L  +L
Sbjct: 643  PSRADQLITYL 653



 Score =  663 bits (1711), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/599 (53%), Positives = 443/599 (73%), Gaps = 14/599 (2%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 43  QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVSTFAEMGVKIYEQTPDAETLL 102

Query: 101 LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           LS+   + SDD  +E  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 103 LSDGPVVASDDQADEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 162

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SN 207
           EEGL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +          ++
Sbjct: 163 EEGLNNMVHAISACPFTIAAILELSGKVASNEISIDDLVDGLSDESIAEAAVAAAADETD 222

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           + V   ++ +++ +   +  S   S E+ L +L+ E L +F+ ++  F+ M +     G 
Sbjct: 223 DSVDSADEADDDSEDSDDEGSTQQSNEKALAQLREECLKRFARVTAQFELMCQESAANGA 282

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S +++ A + +  E+  IRFTAK+IE+LC  ++  +++V  +E+Q+++++V +CGM R 
Sbjct: 283 GSAAFLAARDAVREELRTIRFTAKTIERLCANVQAMVDEVRTVERQVVQLLVERCGMERE 342

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
             I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L L DL+ 
Sbjct: 343 EVIARFPGNETNLAWGQELVAQSRPYSAAVARALPDLEAHQQKLIDIQARAALSLPDLKG 402

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+ FLDLIQEGNIGLMKAVDKFE
Sbjct: 403 VNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFE 462

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+TG EPDP
Sbjct: 463 YRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQTGKEPDP 522

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
           +V+A +++M E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DAAL A +
Sbjct: 523 AVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADAALQAGL 582

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+VV+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA++KLR
Sbjct: 583 RAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKKLR 641


>gi|209519886|ref|ZP_03268669.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
 gi|209499704|gb|EDZ99776.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. H160]
          Length = 665

 Score =  674 bits (1740), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/665 (50%), Positives = 462/665 (69%), Gaps = 33/665 (4%)

Query: 792  DKYDPDSYIRKFGYKIFSKKNA----------FSFDIKSNSREEIENLRKKFKILIKLGK 841
            D+ D       F  K+ S ++A           + D+     EE + L    + LI+LGK
Sbjct: 5    DREDSQHETAAFTAKVPSGRSAKGKSAGKAIPVAADLPPQQAEERQRL---MRALIQLGK 61

Query: 842  ERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSD 897
            E+GYLT ++IND LP++      I+SI+  F  M + V E   D ETL+L++    + SD
Sbjct: 62   EQGYLTHAQINDHLPDNFTQTAAIDSIVSAFSDMGVQVYEQAPDAETLLLNSNAPAVVSD 121

Query: 898  DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHA 957
            D  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR GEI IAKRIE+GL +M+ A
Sbjct: 122  DQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQA 181

Query: 958  ISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL---- 1013
            I++CP  I  IL +A +I+  E++IDE+VDGL ++  ++          + +        
Sbjct: 182  IAACPLAISAILASAQQIADGELRIDELVDGLNEETAAAEEVASADADADEDTDTDEDSE 241

Query: 1014 ---------IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
                      +SS+AD +  +L++L  + L  F+ +   +D+M  +  +    S++Y++A
Sbjct: 242  DEEEDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYDQMNASHTRGDVTSKAYLRA 299

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
              +I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+IVV+K GMPR  FI+ F  
Sbjct: 300  REDIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQIVVSKAGMPREKFIETFAG 359

Query: 1125 NEINLNWVDNETKI-QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             E +L W +   +     Y   L R++P+I+  QQKLI+++  + LPL  L++INR+M+A
Sbjct: 360  TETDLGWTERAARTGASTYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVA 419

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
             E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGNIGLMKAVDKFEYRRG+KF
Sbjct: 420  AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+ILQ+TG E  P+V+A +M
Sbjct: 480  STYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAERM 539

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            E+ EEK+R I+KIAK+PVS+E+PVGDD D+ LGD IED  + +P+DAA+ A +R+ + D 
Sbjct: 540  ELSEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPADAAMQADLRAAIDDA 599

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQIE+KA+RKL HPSR  +L
Sbjct: 600  LDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPSRADRL 659

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 660  KSFLD 664



 Score =  658 bits (1697), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/640 (51%), Positives = 448/640 (70%), Gaps = 23/640 (3%)

Query: 3   FINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
           F  K    ++ K K        + D+     EE + L    + LI+LGKE+GYLT ++IN
Sbjct: 16  FTAKVPSGRSAKGKSAGKAIPVAADLPPQQAEERQRL---MRALIQLGKEQGYLTHAQIN 72

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAAL 118
           D LP++      I+SI+  F  M + V E   D ETL+L++    + SDD  +E TE AL
Sbjct: 73  DHLPDNFTQTAAIDSIVSAFSDMGVQVYEQAPDAETLLLNSNAPAVVSDDQADEETEVAL 132

Query: 119 STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEI 178
           STVDS+FGRT DP++MYMREMG+ ELLTR GEI IAKRIE+GL +M+ AI++CP  I  I
Sbjct: 133 STVDSEFGRTTDPVRMYMREMGATELLTRAGEIAIAKRIEDGLHEMVQAIAACPLAISAI 192

Query: 179 LIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL-------------IE 225
           L +A +I+  E++IDE+VDGL ++  ++          + +                  +
Sbjct: 193 LASAQQIADGELRIDELVDGLNEETAAAEEVASADADADEDTDTDEDSEDEEEDDVGPAD 252

Query: 226 SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
           SS+AD +  +L++L  + L  F+ +   +D+M  +  +    S++Y++A  +I   +  I
Sbjct: 253 SSAADEA--RLKQLTSDCLEIFAQVGILYDQMNASHTRGDVTSKAYLRAREDIQQHLAKI 310

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           RFTA++I++LC  +++Q+ QV  IE+ IL+IVV+K GMPR  FI+ F   E +L W +  
Sbjct: 311 RFTARTIDRLCGDVQHQVAQVRAIERNILQIVVSKAGMPREKFIETFAGTETDLGWTERA 370

Query: 346 TKI-QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
            +     Y   L R++P+I+  QQKLI+++  + LPL  L++INR+M+A E K RKAK E
Sbjct: 371 ARTGASTYGAALERHLPAIQSEQQKLIDIEATVSLPLKHLKEINRQMVAAESKMRKAKSE 430

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           M EANLRLVISIAKKY +RG+ FLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA
Sbjct: 431 MIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQA 490

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           +TRS+ADQARTIR+PVHMIETINK++RISR+ILQ+TG E  P+V+A +ME+ EEK+R I+
Sbjct: 491 VTRSLADQARTIRVPVHMIETINKLNRISREILQQTGQEAHPAVLAERMELSEEKVRGIL 550

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAK+PVS+E+PVGDD D+ LGD IED  + +P+DAA+ A +R+ + D L+SL+PRE+KV
Sbjct: 551 KIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPADAAMQADLRAAIDDALDSLSPREAKV 610

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           LRMR+GI   SDHTLEEVGKQFDVTRERIRQIE+KA+RKL
Sbjct: 611 LRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRKL 650


>gi|377811726|ref|YP_005044166.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. YI23]
 gi|357941087|gb|AET94643.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. YI23]
          Length = 667

 Score =  673 bits (1736), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 330/625 (52%), Positives = 451/625 (72%), Gaps = 22/625 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            E+ E  +++ + LI+LGKERGYLT +EIND LP++  +   +E+++ TF  M ++V E  
Sbjct: 44   EQNEERQRQMRALIQLGKERGYLTHAEINDHLPDNFAETAAMETVVATFNDMGVAVYEQA 103

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+LS+    + +D+  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104  PDAETLLLSDNAPSVVTDEQSDEEAENALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +MI AI++CP+T+  IL  +  +   E+KIDE+VDGL  K   +   
Sbjct: 164  EIAIAKRIEDGLHEMIQAIAACPSTVATILNDSALVESGELKIDELVDGL--KEDDTEEA 221

Query: 1000 VIKGNKNNNEEKILIESS----------------SADLSTEQLEKLKYESLIKFSNISFH 1043
             I   + N+   +  ++                 SA  +  +L++LK + L  F+ +   
Sbjct: 222  EISAPETNDSADVDTDTDESDSDEDDDDDLDGGDSAASNEARLKQLKADCLEIFARVREL 281

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
             +            +++  KA   I  E+  IRFTAK+I++LC  ++ Q+ QV  IE++I
Sbjct: 282  AEHASNPKGSGAVATKAIEKARAEIQRELGSIRFTAKTIDRLCADVQQQVAQVRDIERRI 341

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            L+I V++CGMPR  F++ F  +E +L W         +Y   L R++P+I+  QQKLI++
Sbjct: 342  LQIAVDRCGMPREKFVESFVGHETDLEWTTRAAASAKNYGASLERSLPAIQAEQQKLIDI 401

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +  + +PL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLDLIQE
Sbjct: 402  EGVVEMPLKQLKQINRQMTAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQE 461

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RIS
Sbjct: 462  GNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRIS 521

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            R+ILQ+TG E  PSV+A +MEMPEEKIR I+KIAK+PVS+E+PVG+D D+ LGD IED+ 
Sbjct: 522  REILQQTGQEAHPSVLAERMEMPEEKIRGILKIAKQPVSLETPVGEDADATLGDMIEDQG 581

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
              +P+DAA++A+MR+ + D LN+L+PRE+KVLRMRFGI+ +SD+TLEE+GKQFDVTRERI
Sbjct: 582  AASPADAAVHANMRAAIDDALNALSPREAKVLRMRFGIDTASDYTLEELGKQFDVTRERI 641

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIE+KA+RKL HPSR  KL+ FL+
Sbjct: 642  RQIESKAMRKLMHPSRADKLRPFLD 666



 Score =  656 bits (1693), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/611 (52%), Positives = 441/611 (72%), Gaps = 22/611 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           E+ E  +++ + LI+LGKERGYLT +EIND LP++  +   +E+++ TF  M ++V E  
Sbjct: 44  EQNEERQRQMRALIQLGKERGYLTHAEINDHLPDNFAETAAMETVVATFNDMGVAVYEQA 103

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+LS+    + +D+  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104 PDAETLLLSDNAPSVVTDEQSDEEAENALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +MI AI++CP+T+  IL  +  +   E+KIDE+VDGL  K   +   
Sbjct: 164 EIAIAKRIEDGLHEMIQAIAACPSTVATILNDSALVESGELKIDELVDGL--KEDDTEEA 221

Query: 210 VIKGNKNNNEEKILIESS----------------SADLSTEQLEKLKYESLIKFSNISFH 253
            I   + N+   +  ++                 SA  +  +L++LK + L  F+ +   
Sbjct: 222 EISAPETNDSADVDTDTDESDSDEDDDDDLDGGDSAASNEARLKQLKADCLEIFARVREL 281

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
            +            +++  KA   I  E+  IRFTAK+I++LC  ++ Q+ QV  IE++I
Sbjct: 282 AEHASNPKGSGAVATKAIEKARAEIQRELGSIRFTAKTIDRLCADVQQQVAQVRDIERRI 341

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           L+I V++CGMPR  F++ F  +E +L W         +Y   L R++P+I+  QQKLI++
Sbjct: 342 LQIAVDRCGMPREKFVESFVGHETDLEWTTRAAASAKNYGASLERSLPAIQAEQQKLIDI 401

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +  + +PL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLDLIQE
Sbjct: 402 EGVVEMPLKQLKQINRQMTAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQE 461

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RIS
Sbjct: 462 GNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRIS 521

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           R+ILQ+TG E  PSV+A +MEMPEEKIR I+KIAK+PVS+E+PVG+D D+ LGD IED+ 
Sbjct: 522 REILQQTGQEAHPSVLAERMEMPEEKIRGILKIAKQPVSLETPVGEDADATLGDMIEDQG 581

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
             +P+DAA++A+MR+ + D LN+L+PRE+KVLRMRFGI+ +SD+TLEE+GKQFDVTRERI
Sbjct: 582 AASPADAAVHANMRAAIDDALNALSPREAKVLRMRFGIDTASDYTLEELGKQFDVTRERI 641

Query: 614 RQIEAKALRKL 624
           RQIE+KA+RKL
Sbjct: 642 RQIESKAMRKL 652


>gi|413961233|ref|ZP_11400461.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. SJ98]
 gi|413930105|gb|EKS69392.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. SJ98]
          Length = 668

 Score =  669 bits (1726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/624 (52%), Positives = 453/624 (72%), Gaps = 19/624 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            E+ E  +++ + LI+LGKERGYLT +EIND LP++  +   +E+++ TF  M ++V E  
Sbjct: 44   EQNEERQRQMRALIQLGKERGYLTHAEINDHLPDNFAETAAMETVVSTFHDMGVAVYEQA 103

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+LS+      +D+  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104  PDAETLLLSDNAPSAVTDEQSDEEAENALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +MI AI++CP+T+  IL  A ++   E+KIDE+VDGL +++ +  + 
Sbjct: 164  EIAIAKRIEDGLHEMIQAIAACPSTVATILADAAQVESGELKIDELVDGLKEEDTADEDM 223

Query: 1000 VIKGNKNNNE---------------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHF 1044
                  ++ E               + +     SA  +  +L++LK + L  F+ +    
Sbjct: 224  SASDTTDSAEIDTDTDESDSDEDDDDDLDGAGDSAASNEARLKQLKADCLEIFARVRELA 283

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            ++           +++  KA   I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+++L
Sbjct: 284  EQASSPKGSGAAAAKAVEKARAEIQRELGSIRFTAKTIDRLCANVQQQVAQVRDIERRVL 343

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            +I V++CGMPR  F++ F  +E +L W    +     Y   L R++P+I+  QQKLI+++
Sbjct: 344  QIAVDRCGMPRDKFVESFVGHETDLEWTARASAASKQYGASLERSLPAIQAEQQKLIDIE 403

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
              + +PL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLDLIQEG
Sbjct: 404  GVVEMPLQQLKKINRQMTAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQEG 463

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR
Sbjct: 464  NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISR 523

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            +ILQ+TG E  PSV+A +MEMPEEKIR I+KIAK+PVS+E+PVG+D D+ LGD IED+  
Sbjct: 524  EILQQTGLEAHPSVLAERMEMPEEKIRGILKIAKQPVSLETPVGEDADATLGDMIEDQGA 583

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
             +P++AA++A+MR+ + D LN+L+PRE+KVLRMRFGI+ +SD+TLEE+GKQFDVTRERIR
Sbjct: 584  ASPAEAAVHANMRAAIDDALNALSPREAKVLRMRFGIDTASDYTLEELGKQFDVTRERIR 643

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIE+KA+RKL HPSR  KL+ FL+
Sbjct: 644  QIESKAMRKLMHPSRADKLRPFLD 667



 Score =  652 bits (1683), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/610 (52%), Positives = 443/610 (72%), Gaps = 19/610 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           E+ E  +++ + LI+LGKERGYLT +EIND LP++  +   +E+++ TF  M ++V E  
Sbjct: 44  EQNEERQRQMRALIQLGKERGYLTHAEINDHLPDNFAETAAMETVVSTFHDMGVAVYEQA 103

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+LS+      +D+  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104 PDAETLLLSDNAPSAVTDEQSDEEAENALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +MI AI++CP+T+  IL  A ++   E+KIDE+VDGL +++ +  + 
Sbjct: 164 EIAIAKRIEDGLHEMIQAIAACPSTVATILADAAQVESGELKIDELVDGLKEEDTADEDM 223

Query: 210 VIKGNKNNNE---------------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHF 254
                 ++ E               + +     SA  +  +L++LK + L  F+ +    
Sbjct: 224 SASDTTDSAEIDTDTDESDSDEDDDDDLDGAGDSAASNEARLKQLKADCLEIFARVRELA 283

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           ++           +++  KA   I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+++L
Sbjct: 284 EQASSPKGSGAAAAKAVEKARAEIQRELGSIRFTAKTIDRLCANVQQQVAQVRDIERRVL 343

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           +I V++CGMPR  F++ F  +E +L W    +     Y   L R++P+I+  QQKLI+++
Sbjct: 344 QIAVDRCGMPRDKFVESFVGHETDLEWTARASAASKQYGASLERSLPAIQAEQQKLIDIE 403

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
             + +PL  L+ INR+M A E+K R+AKREM EANLRLVISIAKKY +RG+QFLDLIQEG
Sbjct: 404 GVVEMPLQQLKKINRQMTAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQEG 463

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR
Sbjct: 464 NIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISR 523

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           +ILQ+TG E  PSV+A +MEMPEEKIR I+KIAK+PVS+E+PVG+D D+ LGD IED+  
Sbjct: 524 EILQQTGLEAHPSVLAERMEMPEEKIRGILKIAKQPVSLETPVGEDADATLGDMIEDQGA 583

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
            +P++AA++A+MR+ + D LN+L+PRE+KVLRMRFGI+ +SD+TLEE+GKQFDVTRERIR
Sbjct: 584 ASPAEAAVHANMRAAIDDALNALSPREAKVLRMRFGIDTASDYTLEELGKQFDVTRERIR 643

Query: 615 QIEAKALRKL 624
           QIE+KA+RKL
Sbjct: 644 QIESKAMRKL 653


>gi|323529380|ref|YP_004231532.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. CCGE1001]
 gi|323386382|gb|ADX58472.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1001]
          Length = 664

 Score =  669 bits (1726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/623 (53%), Positives = 452/623 (72%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103  PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL + N ++   
Sbjct: 163  EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEDNVAAEEE 222

Query: 1000 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
             +  + + +E+                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223  NVSADASADEDTDAEDDEDSDGDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +   +S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281  QMNASHTRGDVSSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341  IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521  ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 641  IESKAMRKLMHPSRADRLKSFLD 663



 Score =  652 bits (1683), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/609 (53%), Positives = 442/609 (72%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103 PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL + N ++   
Sbjct: 163 EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEDNVAAEEE 222

Query: 210 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
            +  + + +E+                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223 NVSADASADEDTDAEDDEDSDGDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +   +S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281 QMNASHTRGDVSSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341 IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521 ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 641 IESKAMRKL 649


>gi|407710220|ref|YP_006794084.1| RNA polymerase primary sigma factor [Burkholderia phenoliruptrix
            BR3459a]
 gi|407238903|gb|AFT89101.1| RNA polymerase primary sigma factor [Burkholderia phenoliruptrix
            BR3459a]
          Length = 664

 Score =  668 bits (1723), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/623 (53%), Positives = 451/623 (72%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103  PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL + N ++   
Sbjct: 163  EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEDNVAAEEE 222

Query: 1000 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
             +    + +E+                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223  NVSAEASADEDTDAEDDEDSDGDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +   +S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281  QMNASHTRGDVSSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341  IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521  ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 641  IESKAMRKLMHPSRADRLKSFLD 663



 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/609 (53%), Positives = 441/609 (72%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103 PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL + N ++   
Sbjct: 163 EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEDNVAAEEE 222

Query: 210 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
            +    + +E+                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223 NVSAEASADEDTDAEDDEDSDGDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +   +S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281 QMNASHTRGDVSSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341 IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521 ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 641 IESKAMRKL 649


>gi|339328567|ref|YP_004688259.1| RNA polymerase sigma 70 (sigma D) factor RpoD [Cupriavidus necator
            N-1]
 gi|338171168|gb|AEI82221.1| RNA polymerase sigma 70 (sigma D) factor RpoD [Cupriavidus necator
            N-1]
          Length = 662

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 324/627 (51%), Positives = 451/627 (71%), Gaps = 15/627 (2%)

Query: 816  FDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 875
             DI S +R+E E  +++ + LI LG+ERGYLT ++IND LP++      +E+I+ TF  M
Sbjct: 36   LDIASMARQE-EERQRQMRALIALGRERGYLTHADINDHLPDNFTQTAAMETIVGTFSDM 94

Query: 876  DISVSEHVLDTETLMLSNITSDDDVE----EATEAALSTVDSDFGRTKDPIKMYMREMGS 931
             ++V E   D ETL+L++  +    +    E  EAALSTVDS+FGRT DP++MYMREMG+
Sbjct: 95   GVAVYEQAPDAETLLLNDAAAAAASDDQADEEAEAALSTVDSEFGRTTDPVRMYMREMGA 154

Query: 932  VELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID 991
             ELLTR GEIEIAKRIE+GL+DMI AI++CP+ +  IL+ AD+I   E++IDE+V G+ D
Sbjct: 155  RELLTRAGEIEIAKRIEDGLQDMIQAIATCPSVVSTILVDADRIVAGELRIDELVAGISD 214

Query: 992  K------NFSSNNRVIKGNKNNNEEKIL-IESSSADLST---EQLEKLKYESLIKFSNIS 1041
                      S    +K   ++++     +E  + D  T    +LE+L  +SL  F+ + 
Sbjct: 215  DVNESEMTLESEEVEVKAEASDDDPDRDDVEMDAGDPETTNAARLEQLTSDSLAVFARVR 274

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              F+++          S +  +  + I  E+  IRFTA++I++LC ++R Q  +V  IE+
Sbjct: 275  ALFEQLPDVPVTGKTRSAAVAQLRSAIQRELAPIRFTARTIDRLCASVRAQTTEVRAIER 334

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
             ILEI V++CGMPR  F++ FP  E +L W          +   L R++P+I+  QQKLI
Sbjct: 335  GILEITVDRCGMPRDVFVESFPGYETDLTWTCRMAATSRHFGTALERHLPAIQAGQQKLI 394

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++  + LPL  L+ INR+M+A E+K R+AKREM EANLRLVISIAKKY +RG+QFLDLI
Sbjct: 395  EIEARVSLPLQQLKQINRQMVAAELKMRQAKREMIEANLRLVISIAKKYVNRGMQFLDLI 454

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLM+AVDKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHMIE +NK++R
Sbjct: 455  QEGNIGLMRAVDKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMIEMVNKLNR 514

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISR+ LQ+TG E  P+++A +MEM EEK+R I++IA++PVS+E+PVGDD D+ LGD IED
Sbjct: 515  ISREFLQQTGQEAHPAILAERMEMSEEKVRSILRIARQPVSLETPVGDDADATLGDMIED 574

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
             +  +P++AA++ +MR+ + + L+ L+PRE+KVLRMRFG++ +SDHTLEEVGKQFDVTRE
Sbjct: 575  VSASSPTEAAIHGNMRAAIDEALDELSPREAKVLRMRFGLDTTSDHTLEEVGKQFDVTRE 634

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIE+KA+RKL HPSR  KL+ FLE
Sbjct: 635  RIRQIESKAMRKLMHPSRADKLRPFLE 661



 Score =  652 bits (1682), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/637 (50%), Positives = 448/637 (70%), Gaps = 15/637 (2%)

Query: 2   KFINKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEI 61
           + I   +K   +  KE         DI S +R+E E  +++ + LI LG+ERGYLT ++I
Sbjct: 12  RVIAVTSKAGRRAPKEKTQAVTIPLDIASMARQE-EERQRQMRALIALGRERGYLTHADI 70

Query: 62  NDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVE----EATEAA 117
           ND LP++      +E+I+ TF  M ++V E   D ETL+L++  +    +    E  EAA
Sbjct: 71  NDHLPDNFTQTAAMETIVGTFSDMGVAVYEQAPDAETLLLNDAAAAAASDDQADEEAEAA 130

Query: 118 LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 177
           LSTVDS+FGRT DP++MYMREMG+ ELLTR GEIEIAKRIE+GL+DMI AI++CP+ +  
Sbjct: 131 LSTVDSEFGRTTDPVRMYMREMGARELLTRAGEIEIAKRIEDGLQDMIQAIATCPSVVST 190

Query: 178 ILIAADKISKNEIKIDEIVDGLIDK------NFSSNNRVIKGNKNNNEEKIL-IESSSAD 230
           IL+ AD+I   E++IDE+V G+ D          S    +K   ++++     +E  + D
Sbjct: 191 ILVDADRIVAGELRIDELVAGISDDVNESEMTLESEEVEVKAEASDDDPDRDDVEMDAGD 250

Query: 231 LST---EQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRF 287
             T    +LE+L  +SL  F+ +   F+++          S +  +  + I  E+  IRF
Sbjct: 251 PETTNAARLEQLTSDSLAVFARVRALFEQLPDVPVTGKTRSAAVAQLRSAIQRELAPIRF 310

Query: 288 TAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETK 347
           TA++I++LC ++R Q  +V  IE+ ILEI V++CGMPR  F++ FP  E +L W      
Sbjct: 311 TARTIDRLCASVRAQTTEVRAIERGILEITVDRCGMPRDVFVESFPGYETDLTWTCRMAA 370

Query: 348 IQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTE 407
               +   L R++P+I+  QQKLI ++  + LPL  L+ INR+M+A E+K R+AKREM E
Sbjct: 371 TSRHFGTALERHLPAIQAGQQKLIEIEARVSLPLQQLKQINRQMVAAELKMRQAKREMIE 430

Query: 408 ANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467
           ANLRLVISIAKKY +RG+QFLDLIQEGNIGLM+AVDKFEYRRG+KFSTYATWW+RQA+TR
Sbjct: 431 ANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMRAVDKFEYRRGWKFSTYATWWVRQAVTR 490

Query: 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA 527
           ++ADQARTIR+PVHMIE +NK++RISR+ LQ+TG E  P+++A +MEM EEK+R I++IA
Sbjct: 491 ALADQARTIRVPVHMIEMVNKLNRISREFLQQTGQEAHPAILAERMEMSEEKVRSILRIA 550

Query: 528 KEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRM 587
           ++PVS+E+PVGDD D+ LGD IED +  +P++AA++ +MR+ + + L+ L+PRE+KVLRM
Sbjct: 551 RQPVSLETPVGDDADATLGDMIEDVSASSPTEAAIHGNMRAAIDEALDELSPREAKVLRM 610

Query: 588 RFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           RFG++ +SDHTLEEVGKQFDVTRERIRQIE+KA+RKL
Sbjct: 611 RFGLDTTSDHTLEEVGKQFDVTRERIRQIESKAMRKL 647


>gi|385206021|ref|ZP_10032891.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
 gi|385185912|gb|EIF35186.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
          Length = 705

 Score =  664 bits (1713), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/635 (50%), Positives = 448/635 (70%), Gaps = 12/635 (1%)

Query: 806  KIFSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEII 865
            K  ++ +A    +   S  E E+ R   + LIKLG ERG++   EI+D LPE +   + I
Sbjct: 69   KANTRVHAAIASLPDESSGENESGRADLRALIKLGTERGFVIRGEISDCLPERLAQPDAI 128

Query: 866  ESIIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPI 922
            E++I+ F  M I+V E   D E+++L   + +++DD +EE    A+S+VD++FGRT DP+
Sbjct: 129  ENVIRAFSEMGIAVFEQAPDAESMILHDRAAVSADDQIEEEAVTAISSVDAEFGRTTDPV 188

Query: 923  KMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKI 982
            +MYMREMG+ ELLTR GEI +A+RIEEG   MI AISSCP TI EIL  AD ++  E  I
Sbjct: 189  RMYMREMGTTELLTRQGEIALARRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAI 248

Query: 983  DEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL---------STEQLEKLKYES 1033
            DE+VDGLID   +  + +    +++ +   + +    D          + + +E LK+++
Sbjct: 249  DELVDGLIDPAATGTDGMTAVPEDSLDTASVFDDDQGDEDDDDTETEPADQYIETLKHDA 308

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
            L KF+ ++  F ++R A+E +GY    Y  A   I  E++ IRFTA++I++LC  LR   
Sbjct: 309  LAKFAKVADWFGQLRDAYETQGYGCARYRAAQAAIEAELMTIRFTARTIDRLCGALRLSA 368

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
            ++V  IE++I  IVV +CG+PR  F+  F  NE +L W          ++ +L RN+P+I
Sbjct: 369  DEVRTIEREIARIVVERCGVPRDTFVAHFRGNETHLAWARQLVAAGQPFSSVLERNLPAI 428

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
               Q+KL+ LQ  +VLPL++ R++ R + A E K  +AK EM EANLRLVISIAK+YT+R
Sbjct: 429  DLEQEKLLALQQRVVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNR 488

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GL FLDLIQEGNIGLM+AVDKFEYRRGYKFSTYATWWIRQA++RSIADQARTIR+PVHMI
Sbjct: 489  GLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVHMI 548

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            E++NK+ RISRQILQETGSEPD +++A +MEM E+K+R +++I +EPVS+++ VG+++D+
Sbjct: 549  ESLNKLKRISRQILQETGSEPDAALLAQRMEMQEQKVRAMLRIVREPVSLDASVGENDDT 608

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
             +GD IED   + P DAAL+ASMR  + + L +LTPRE+K+LR+RFGIE   DHTLEE+G
Sbjct: 609  SIGDLIEDSTAILPDDAALHASMRDAISEALMTLTPREAKILRLRFGIESGRDHTLEELG 668

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            +QF++TRERIRQIE KALRKLRHP+R  +LK FL+
Sbjct: 669  EQFELTRERIRQIEVKALRKLRHPARSERLKSFLD 703



 Score =  650 bits (1677), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 315/629 (50%), Positives = 441/629 (70%), Gaps = 12/629 (1%)

Query: 9   KIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPED 68
           +  +++TK     +A    +   S  E E+ R   + LIKLG ERG++   EI+D LPE 
Sbjct: 62  RAASRRTKANTRVHAAIASLPDESSGENESGRADLRALIKLGTERGFVIRGEISDCLPER 121

Query: 69  IIDHEIIESIIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDF 125
           +   + IE++I+ F  M I+V E   D E+++L   + +++DD +EE    A+S+VD++F
Sbjct: 122 LAQPDAIENVIRAFSEMGIAVFEQAPDAESMILHDRAAVSADDQIEEEAVTAISSVDAEF 181

Query: 126 GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 185
           GRT DP++MYMREMG+ ELLTR GEI +A+RIEEG   MI AISSCP TI EIL  AD +
Sbjct: 182 GRTTDPVRMYMREMGTTELLTRQGEIALARRIEEGRNGMIRAISSCPATIAEILAIADGV 241

Query: 186 SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL---------STEQL 236
           +  E  IDE+VDGLID   +  + +    +++ +   + +    D          + + +
Sbjct: 242 ACGETAIDELVDGLIDPAATGTDGMTAVPEDSLDTASVFDDDQGDEDDDDTETEPADQYI 301

Query: 237 EKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLC 296
           E LK+++L KF+ ++  F ++R A+E +GY    Y  A   I  E++ IRFTA++I++LC
Sbjct: 302 ETLKHDALAKFAKVADWFGQLRDAYETQGYGCARYRAAQAAIEAELMTIRFTARTIDRLC 361

Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 356
             LR   ++V  IE++I  IVV +CG+PR  F+  F  NE +L W          ++ +L
Sbjct: 362 GALRLSADEVRTIEREIARIVVERCGVPRDTFVAHFRGNETHLAWARQLVAAGQPFSSVL 421

Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
            RN+P+I   Q+KL+ LQ  +VLPL++ R++ R + A E K  +AK EM EANLRLVISI
Sbjct: 422 ERNLPAIDLEQEKLLALQQRVVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISI 481

Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
           AK+YT+RGL FLDLIQEGNIGLM+AVDKFEYRRGYKFSTYATWWIRQA++RSIADQARTI
Sbjct: 482 AKRYTNRGLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTI 541

Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536
           R+PVHMIE++NK+ RISRQILQETGSEPD +++A +MEM E+K+R +++I +EPVS+++ 
Sbjct: 542 RVPVHMIESLNKLKRISRQILQETGSEPDAALLAQRMEMQEQKVRAMLRIVREPVSLDAS 601

Query: 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596
           VG+++D+ +GD IED   + P DAAL+ASMR  + + L +LTPRE+K+LR+RFGIE   D
Sbjct: 602 VGENDDTSIGDLIEDSTAILPDDAALHASMRDAISEALMTLTPREAKILRLRFGIESGRD 661

Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           HTLEE+G+QF++TRERIRQIE KALRKLR
Sbjct: 662 HTLEELGEQFELTRERIRQIEVKALRKLR 690


>gi|91777566|ref|YP_552774.1| sigma70 factor RpoD [Burkholderia xenovorans LB400]
 gi|91690226|gb|ABE33424.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
            LB400]
          Length = 665

 Score =  664 bits (1713), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 329/623 (52%), Positives = 445/623 (71%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104  PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164  EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTIAAEED 223

Query: 1000 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
                  +   +                  +SS+AD +  +L++L  + L  F+ +    D
Sbjct: 224  SASAEASAEVDADTDGDEDEDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282  QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342  IVVSKSGMPREKFIESFAGHEADLGWTERAARGASAYGAALERHLPAIQSEQQKLIEIEA 401

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522  ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 642  IESKAMRKLMHPSRADRLKSFLD 664



 Score =  648 bits (1671), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/609 (52%), Positives = 435/609 (71%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104 PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164 EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTIAAEED 223

Query: 210 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
                 +   +                  +SS+AD +  +L++L  + L  F+ +    D
Sbjct: 224 SASAEASAEVDADTDGDEDEDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAARGASAYGAALERHLPAIQSEQQKLIEIEA 401

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522 ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 642 IESKAMRKL 650


>gi|187921222|ref|YP_001890254.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia phytofirmans PsJN]
 gi|187719660|gb|ACD20883.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phytofirmans
            PsJN]
          Length = 665

 Score =  662 bits (1709), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 329/623 (52%), Positives = 447/623 (71%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104  PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164  EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTLAAEED 223

Query: 1000 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
                + + + +                  +SS+AD +  +L++L  + L  F+ +    D
Sbjct: 224  STGADASADVDADTDSDDDEDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282  QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342  IVVSKSGMPREKFIESFAGHEADLGWTERAARGASSYGAALERHLPAIQSEQQKLIEIEA 401

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522  ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 642  IESKAMRKLMHPSRADRLKSFLD 664



 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/609 (52%), Positives = 437/609 (71%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104 PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164 EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTLAAEED 223

Query: 210 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
               + + + +                  +SS+AD +  +L++L  + L  F+ +    D
Sbjct: 224 STGADASADVDADTDSDDDEDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAARGASSYGAALERHLPAIQSEQQKLIEIEA 401

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522 ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 642 IESKAMRKL 650


>gi|307726409|ref|YP_003909622.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
 gi|307586934|gb|ADN60331.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1003]
          Length = 664

 Score =  662 bits (1708), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 330/623 (52%), Positives = 451/623 (72%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103  PDAETLLLNSNTPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL ++N ++   
Sbjct: 163  EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEENVAAEEE 222

Query: 1000 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
             +  +   +++                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223  TVSADSAADDDADADEDEDSDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +    S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281  RMNASHTRGDVTSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341  IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521  ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 641  IESKAMRKLMHPSRADRLKSFLD 663



 Score =  646 bits (1666), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/609 (52%), Positives = 441/609 (72%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 43  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFTQTAAIDSIVSAFNDMGVQVYEQA 102

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 103 PDAETLLLNSNTPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 162

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI+ CP  I  IL +A +++  E++IDE+VDGL ++N ++   
Sbjct: 163 EIAIAKRIEDGLHEMVQAIAGCPLAISAILASAQQVADGELRIDELVDGLNEENVAAEEE 222

Query: 210 VIKGNKNNNEEKIL--------------IESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
            +  +   +++                  +SS+AD +  +L++L  + L  F+ +   +D
Sbjct: 223 TVSADSAADDDADADEDEDSDSDDDVGPADSSAADEA--RLKQLTSDCLEIFAQVGILYD 280

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +    S++Y KA   I   +  IRFTA++I++LC  +++Q+ QV  IE+ IL+
Sbjct: 281 RMNASHTRGDVTSKAYQKAREEIQQHLAKIRFTARTIDRLCGDVQHQVAQVRAIERNILQ 340

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI+++ 
Sbjct: 341 IVVTKSGMPREKFIESFSGHEADLGWTERAARGNTSYGAALERHLPAIQSEQQKLIDIEA 400

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 401 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 460

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 461 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 520

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +M++ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 521 ILQQTGQEAHPSVLAERMDLSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 580

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 581 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 640

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 641 IESKAMRKL 649


>gi|422349725|ref|ZP_16430614.1| RNA polymerase sigma factor RpoD [Sutterella wadsworthensis
            2_1_59BFAA]
 gi|404657934|gb|EKB30814.1| RNA polymerase sigma factor RpoD [Sutterella wadsworthensis
            2_1_59BFAA]
          Length = 813

 Score =  660 bits (1703), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/622 (54%), Positives = 451/622 (72%), Gaps = 11/622 (1%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K A      S+  +  E+ R K   LI++G+ERGY+T+ EIND LP  +ID + IE+++ 
Sbjct: 196  KKALLNGYGSDEEDSTEDRRSKLFTLIRMGRERGYVTYGEINDNLPNSLIDDDAIETVVA 255

Query: 871  TFRYMDISVSEHVLDTETL-MLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMR 927
                + I V E   D +TL M+ N  + S++D +   EAALSTVDS+FGRT DP+++YMR
Sbjct: 256  ILSNLHIQVFESAPDEDTLAMMGNESVASEEDADAEAEAALSTVDSEFGRTTDPVRIYMR 315

Query: 928  EMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD 987
            EMGSVELL+R+GEIEI+KRIE+GLK M+ AIS CP T+  I+  A +I +  + ID+IVD
Sbjct: 316  EMGSVELLSREGEIEISKRIEDGLKHMVLAISRCPVTVAAIVGYAHEIREGTLPIDDIVD 375

Query: 988  GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
            GL+  + + N   + G+ N++E  +     ++ ++ +QLE +K  SL  F+ +  HF+ +
Sbjct: 376  GLVAADDTGN---VLGH-NDDETDM----GASAMTVDQLEDMKQRSLAIFAVVEEHFNTL 427

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            +    +EGY S+      ++I  E++ +RFTAK+ +KLC+ LR  I++V   +K I   +
Sbjct: 428  KTVVREEGYGSDRLDPLKDSIQRELMAVRFTAKTADKLCELLRTTIDEVRTRQKTIYNEL 487

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V + G+ R  F+  F ++  +L+W+    +   +    L    P+++E Q+KL  L ++ 
Sbjct: 488  VRRVGLDRTWFLATFADHATDLDWMSAIVRDNPEKAAYLEHLRPTVEEEQRKLAELVSNA 547

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             + + +L D  ++M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGN+G
Sbjct: 548  CMTVPELFDTYKQMATGEAKARNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVG 607

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN+++RI+RQIL
Sbjct: 608  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINRMNRITRQIL 667

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QETG EPD   +A  ME+PE+KI KIMKIAKEP+SME+P+GDD+DSHLGDF+ED   +AP
Sbjct: 668  QETGVEPDSRELAKLMELPEDKILKIMKIAKEPISMETPIGDDDDSHLGDFLEDTQTVAP 727

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            ++A  N S+   V+ +L+SL+PRE+KVLRMRFGIEM SDHTLEEVGKQFDVTRERIRQIE
Sbjct: 728  AEAIQNTSLSETVRQVLDSLSPREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQIE 787

Query: 1408 AKALRKLRHPSRYYKLKIFLEG 1429
             KALRKLRHPSR  KL+ F+EG
Sbjct: 788  TKALRKLRHPSRADKLRSFVEG 809



 Score =  640 bits (1651), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 328/608 (53%), Positives = 440/608 (72%), Gaps = 11/608 (1%)

Query: 21  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 80
           K A      S+  +  E+ R K   LI++G+ERGY+T+ EIND LP  +ID + IE+++ 
Sbjct: 196 KKALLNGYGSDEEDSTEDRRSKLFTLIRMGRERGYVTYGEINDNLPNSLIDDDAIETVVA 255

Query: 81  TFRYMDISVSEHVLDTETL-MLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMR 137
               + I V E   D +TL M+ N  + S++D +   EAALSTVDS+FGRT DP+++YMR
Sbjct: 256 ILSNLHIQVFESAPDEDTLAMMGNESVASEEDADAEAEAALSTVDSEFGRTTDPVRIYMR 315

Query: 138 EMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD 197
           EMGSVELL+R+GEIEI+KRIE+GLK M+ AIS CP T+  I+  A +I +  + ID+IVD
Sbjct: 316 EMGSVELLSREGEIEISKRIEDGLKHMVLAISRCPVTVAAIVGYAHEIREGTLPIDDIVD 375

Query: 198 GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
           GL+  + + N   + G+ N++E  +     ++ ++ +QLE +K  SL  F+ +  HF+ +
Sbjct: 376 GLVAADDTGN---VLGH-NDDETDM----GASAMTVDQLEDMKQRSLAIFAVVEEHFNTL 427

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           +    +EGY S+      ++I  E++ +RFTAK+ +KLC+ LR  I++V   +K I   +
Sbjct: 428 KTVVREEGYGSDRLDPLKDSIQRELMAVRFTAKTADKLCELLRTTIDEVRTRQKTIYNEL 487

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V + G+ R  F+  F ++  +L+W+    +   +    L    P+++E Q+KL  L ++ 
Sbjct: 488 VRRVGLDRTWFLATFADHATDLDWMSAIVRDNPEKAAYLEHLRPTVEEEQRKLAELVSNA 547

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            + + +L D  ++M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGN+G
Sbjct: 548 CMTVPELFDTYKQMATGEAKARNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVG 607

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN+++RI+RQIL
Sbjct: 608 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINRMNRITRQIL 667

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QETG EPD   +A  ME+PE+KI KIMKIAKEP+SME+P+GDD+DSHLGDF+ED   +AP
Sbjct: 668 QETGVEPDSRELAKLMELPEDKILKIMKIAKEPISMETPIGDDDDSHLGDFLEDTQTVAP 727

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           ++A  N S+   V+ +L+SL+PRE+KVLRMRFGIEM SDHTLEEVGKQFDVTRERIRQIE
Sbjct: 728 AEAIQNTSLSETVRQVLDSLSPREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQIE 787

Query: 618 AKALRKLR 625
            KALRKLR
Sbjct: 788 TKALRKLR 795


>gi|261380693|ref|ZP_05985266.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
 gi|284796404|gb|EFC51751.1| RNA polymerase sigma factor RpoD [Neisseria subflava NJ9703]
          Length = 650

 Score =  659 bits (1700), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/629 (54%), Positives = 454/629 (72%), Gaps = 23/629 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81   AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
             IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140  IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 1002 KGN----KNNNEE--------------KILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
             G+    K ++EE              +    + S  +S   L +LK + L  F+ I   
Sbjct: 200  LGHLENAKPDDEEGETDSDDEDGDEEDEDDSGNDSEAISAAHLAELKQKVLEHFAFIESE 259

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260  YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI+ F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320  RDICIDRVRMERDYFIENFLPAITDLEWVEKEVAKGRVWANALDRFRHAILEKQAELANM 379

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +T+  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380  ETETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560  NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            RQIEAKALRKLRHP+R  +L+ FL+ ++N
Sbjct: 620  RQIEAKALRKLRHPTRSDRLRSFLDSEEN 648



 Score =  642 bits (1656), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/620 (54%), Positives = 444/620 (71%), Gaps = 24/620 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81  AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
            IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140 IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 212 KGN----KNNNEE--------------KILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
            G+    K ++EE              +    + S  +S   L +LK + L  F+ I   
Sbjct: 200 LGHLENAKPDDEEGETDSDDEDGDEEDEDDSGNDSEAISAAHLAELKQKVLEHFAFIESE 259

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260 YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI+ F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320 RDICIDRVRMERDYFIENFLPAITDLEWVEKEVAKGRVWANALDRFRHAILEKQAELANM 379

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +T+  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380 ETETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560 NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 620 RQIEAKALRKLRHPTRSDRL 639


>gi|91779751|ref|YP_554959.1| sigma70 factor RpoD [Burkholderia xenovorans LB400]
 gi|91692411|gb|ABE35609.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
            LB400]
          Length = 647

 Score =  659 bits (1700), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/630 (50%), Positives = 445/630 (70%), Gaps = 13/630 (2%)

Query: 812  NAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKT 871
            N      +S    E E+ R   K LIKLG ERG++   EI+D LPE +   + IE++++ 
Sbjct: 16   NDLGMQDESGKENENESGRADLKALIKLGTERGFVIRGEISDCLPERLAQPDAIENVVRA 75

Query: 872  FRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMR 927
            F  M I+V E   D E++++++    + +D+ +EE    A+S+VD++FGRT DP++MYMR
Sbjct: 76   FSEMGIAVFEQAPDAESMIMNDHPAAVATDEQIEEEAVTAISSVDAEFGRTTDPVRMYMR 135

Query: 928  EMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD 987
            EMG+ ELLTR GEI +A+RIEEG   MI AISSCP TI EIL  AD ++  E  IDE VD
Sbjct: 136  EMGTTELLTRQGEIALAQRIEEGRNGMIRAISSCPATIAEILAIADGVACGETAIDEFVD 195

Query: 988  GLIDKNFSSNNRVIKGNKNN---------NEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            GL+D   ++ + +I   +++         ++     + + A+ + + +E LK+++L KF+
Sbjct: 196  GLVDPAATATDDMIAVPEDSLGATPMFDDDQGDEDDDGAEAEPADQHIETLKHDALAKFA 255

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             ++  F ++R A+E +GY S  Y  A   I  E++ IRFTA++IE+LC  LR   ++V  
Sbjct: 256  KVADWFSQLRDAYETQGYGSARYRAAQAAIEAELMTIRFTARTIERLCGALRLSADEVRT 315

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            IE++I  I V +CG+PR  FI  F  NE +  W          ++ +L RN+P+I   Q+
Sbjct: 316  IEREIARIAVERCGVPRDTFIAHFRGNETDPAWARQLAAAGQPFSSVLERNLPAIGLEQE 375

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KL+ LQ  +VLPL++ R++ R + A E K  +AK EM EANLRLVISIAK+YT+RGL FL
Sbjct: 376  KLLALQKRVVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFL 435

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLM+AVDKFEYRRGYKFSTYATWWIRQA++RSIADQARTIR+PVHMIE++NK
Sbjct: 436  DLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVHMIESLNK 495

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            + RISR+ILQETG+EPD +++A  MEM E+K+R +++I KEPVS+++ VG+++D+ +GD 
Sbjct: 496  LKRISRKILQETGNEPDAALLAQLMEMQEQKVRAMLRIVKEPVSLDASVGENDDTSIGDL 555

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED   + P DAAL+A MR  + + L +LTPRE+K+LR+RFGIE S DHTLEE+G+QF++
Sbjct: 556  IEDSAAILPDDAALHAGMRDAISEALMTLTPREAKILRLRFGIESSRDHTLEELGEQFEL 615

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIE KALRKLRHP+R  +LK FL+
Sbjct: 616  TRERIRQIEVKALRKLRHPARSARLKSFLD 645



 Score =  642 bits (1657), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 314/631 (49%), Positives = 440/631 (69%), Gaps = 13/631 (2%)

Query: 8   TKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPE 67
           TK   K+    +  N      +S    E E+ R   K LIKLG ERG++   EI+D LPE
Sbjct: 2   TKRVVKRRALDVAANDLGMQDESGKENENESGRADLKALIKLGTERGFVIRGEISDCLPE 61

Query: 68  DIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDS 123
            +   + IE++++ F  M I+V E   D E++++++    + +D+ +EE    A+S+VD+
Sbjct: 62  RLAQPDAIENVVRAFSEMGIAVFEQAPDAESMIMNDHPAAVATDEQIEEEAVTAISSVDA 121

Query: 124 DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 183
           +FGRT DP++MYMREMG+ ELLTR GEI +A+RIEEG   MI AISSCP TI EIL  AD
Sbjct: 122 EFGRTTDPVRMYMREMGTTELLTRQGEIALAQRIEEGRNGMIRAISSCPATIAEILAIAD 181

Query: 184 KISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN---------NEEKILIESSSADLSTE 234
            ++  E  IDE VDGL+D   ++ + +I   +++         ++     + + A+ + +
Sbjct: 182 GVACGETAIDEFVDGLVDPAATATDDMIAVPEDSLGATPMFDDDQGDEDDDGAEAEPADQ 241

Query: 235 QLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEK 294
            +E LK+++L KF+ ++  F ++R A+E +GY S  Y  A   I  E++ IRFTA++IE+
Sbjct: 242 HIETLKHDALAKFAKVADWFSQLRDAYETQGYGSARYRAAQAAIEAELMTIRFTARTIER 301

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNL 354
           LC  LR   ++V  IE++I  I V +CG+PR  FI  F  NE +  W          ++ 
Sbjct: 302 LCGALRLSADEVRTIEREIARIAVERCGVPRDTFIAHFRGNETDPAWARQLAAAGQPFSS 361

Query: 355 ILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVI 414
           +L RN+P+I   Q+KL+ LQ  +VLPL++ R++ R + A E K  +AK EM EANLRLVI
Sbjct: 362 VLERNLPAIGLEQEKLLALQKRVVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVI 421

Query: 415 SIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474
           SIAK+YT+RGL FLDLIQEGNIGLM+AVDKFEYRRGYKFSTYATWWIRQA++RSIADQAR
Sbjct: 422 SIAKRYTNRGLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQAR 481

Query: 475 TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 534
           TIR+PVHMIE++NK+ RISR+ILQETG+EPD +++A  MEM E+K+R +++I KEPVS++
Sbjct: 482 TIRVPVHMIESLNKLKRISRKILQETGNEPDAALLAQLMEMQEQKVRAMLRIVKEPVSLD 541

Query: 535 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMS 594
           + VG+++D+ +GD IED   + P DAAL+A MR  + + L +LTPRE+K+LR+RFGIE S
Sbjct: 542 ASVGENDDTSIGDLIEDSAAILPDDAALHAGMRDAISEALMTLTPREAKILRLRFGIESS 601

Query: 595 SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            DHTLEE+G+QF++TRERIRQIE KALRKLR
Sbjct: 602 RDHTLEELGEQFELTRERIRQIEVKALRKLR 632


>gi|350571066|ref|ZP_08939404.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria wadsworthii
            9715]
 gi|349793433|gb|EGZ47267.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria wadsworthii
            9715]
          Length = 651

 Score =  659 bits (1700), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 342/637 (53%), Positives = 454/637 (71%), Gaps = 42/637 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + + LI +GK+RGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 25   EEQRARLRQLIIMGKDRGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 84

Query: 887  ETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++++    IT DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 85   DTLLMNDNSTGITDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 143

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+MI AIS+CP +I EIL   +++  +EIK+DE V+ +ID N    N +  
Sbjct: 144  IAKKIENALKNMIQAISACPGSIAEILALIEQVRNDEIKVDEAVEAIIDPNEVLLNELGL 203

Query: 1003 GNKNNNEEKILIESSSAD-------------------------LSTEQLEKLKYESLIKF 1037
            G+         +E+++AD                         L    LE+LK + L  F
Sbjct: 204  GH---------LETATADSSGESSDDEAEDDSEDEDEEDNGGTLENTNLEELKQKVLEHF 254

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              I+  ++KM  A +K       Y+K  + I+N++L +RF+ + IE L   LRN ++Q+ 
Sbjct: 255  DGINESYEKMIAALDKYDSKHPKYLKHRDAIANKLLEVRFSTRQIENLSSNLRNNVDQIR 314

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            ++E++I +I +++  M R +FI  F  N  NL+WV  E      ++  L R   +I E Q
Sbjct: 315  KLEREIRDICLDRVHMDRDYFIASFLPNTTNLDWVGEEISKNRVWSDALSRFQHAILEKQ 374

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             ++  ++    + +++L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQF
Sbjct: 375  TEMAGMEKQARISIDELKEINKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQF 434

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 435  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 494

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RI+RQ LQ+ G EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 495  KMNRIARQYLQDNGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 554

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N +APSDAA+ +S+R V KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 555  FIEDINNVAPSDAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 614

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFL---EGKK 1431
            VTRERIRQIEAKALRKLRHP+R  +LK FL   EGK+
Sbjct: 615  VTRERIRQIEAKALRKLRHPTRSDRLKSFLDSEEGKQ 651



 Score =  642 bits (1657), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/626 (53%), Positives = 444/626 (70%), Gaps = 40/626 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + + LI +GK+RGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 25  EEQRARLRQLIIMGKDRGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 84

Query: 97  ETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++++    IT DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 85  DTLLMNDNSTGITDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 143

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+MI AIS+CP +I EIL   +++  +EIK+DE V+ +ID N    N +  
Sbjct: 144 IAKKIENALKNMIQAISACPGSIAEILALIEQVRNDEIKVDEAVEAIIDPNEVLLNELGL 203

Query: 213 GNKNNNEEKILIESSSAD-------------------------LSTEQLEKLKYESLIKF 247
           G+         +E+++AD                         L    LE+LK + L  F
Sbjct: 204 GH---------LETATADSSGESSDDEAEDDSEDEDEEDNGGTLENTNLEELKQKVLEHF 254

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
             I+  ++KM  A +K       Y+K  + I+N++L +RF+ + IE L   LRN ++Q+ 
Sbjct: 255 DGINESYEKMIAALDKYDSKHPKYLKHRDAIANKLLEVRFSTRQIENLSSNLRNNVDQIR 314

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
           ++E++I +I +++  M R +FI  F  N  NL+WV  E      ++  L R   +I E Q
Sbjct: 315 KLEREIRDICLDRVHMDRDYFIASFLPNTTNLDWVGEEISKNRVWSDALSRFQHAILEKQ 374

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            ++  ++    + +++L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQF
Sbjct: 375 TEMAGMEKQARISIDELKEINKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQF 434

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 435 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 494

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RI+RQ LQ+ G EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGD
Sbjct: 495 KMNRIARQYLQDNGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGD 554

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED N +APSDAA+ +S+R V KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 555 FIEDINNVAPSDAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 614

Query: 608 VTRERIRQIEAKALRKLR-PLAHDWL 632
           VTRERIRQIEAKALRKLR P   D L
Sbjct: 615 VTRERIRQIEAKALRKLRHPTRSDRL 640


>gi|241760450|ref|ZP_04758543.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
 gi|241318954|gb|EER55456.1| RNA polymerase sigma factor RpoD [Neisseria flavescens SK114]
          Length = 650

 Score =  659 bits (1699), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/629 (54%), Positives = 453/629 (72%), Gaps = 23/629 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81   AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
             IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140  IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 1002 KGN----KNNNEE--------------KILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
             G+    K +NEE              +    S S  +S   L +LK + L  F+ I   
Sbjct: 200  LGHLENAKPDNEEGETDSDDEDGDDEDEDGSGSDSEAISAAHLAELKQKVLEHFAFIESE 259

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260  YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FIK F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320  RDICIDRVRMERDYFIKNFLPAITDLKWVEEEVAKGRVWANALDRFRHAILEKQTELANM 379

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380  EAETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560  NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            RQIEAKALRKLRHP+R  +L+ FL+ ++N
Sbjct: 620  RQIEAKALRKLRHPTRSDRLRSFLDSEEN 648



 Score =  641 bits (1654), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 339/620 (54%), Positives = 443/620 (71%), Gaps = 24/620 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81  AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
            IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140 IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 212 KGN----KNNNEE--------------KILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
            G+    K +NEE              +    S S  +S   L +LK + L  F+ I   
Sbjct: 200 LGHLENAKPDNEEGETDSDDEDGDDEDEDGSGSDSEAISAAHLAELKQKVLEHFAFIESE 259

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260 YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FIK F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320 RDICIDRVRMERDYFIKNFLPAITDLKWVEEEVAKGRVWANALDRFRHAILEKQTELANM 379

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380 EAETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560 NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 620 RQIEAKALRKLRHPTRSDRL 639


>gi|319638161|ref|ZP_07992924.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
 gi|317400434|gb|EFV81092.1| RNA polymerase sigma factor rpoD [Neisseria mucosa C102]
          Length = 650

 Score =  657 bits (1696), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/629 (54%), Positives = 452/629 (71%), Gaps = 23/629 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81   AEDILLSDNAAALTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV- 1000
             IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140  IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 1001 ---IKGNKNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFH 1043
               ++  K ++EE         D              +S   L +LK + L  F+ I   
Sbjct: 200  LGHLENTKPDDEEGETDSEVEDDDEDDEDDSGSDSEAMSAAHLAELKQKVLEHFAFIESE 259

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260  YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI+ F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320  RDICIDRVRMERDYFIENFLPAITDLEWVEKEVAKGRVWANALDRFRHAILEKQAELANM 379

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +T+  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380  ETETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560  NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            RQIEAKALRKLRHP+R  +L+ FL+ ++N
Sbjct: 620  RQIEAKALRKLRHPTRSDRLRSFLDSEEN 648



 Score =  640 bits (1652), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 336/620 (54%), Positives = 442/620 (71%), Gaps = 24/620 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81  AEDILLSDNAAALTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV- 210
            IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140 IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 211 ---IKGNKNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFH 253
              ++  K ++EE         D              +S   L +LK + L  F+ I   
Sbjct: 200 LGHLENTKPDDEEGETDSEVEDDDEDDEDDSGSDSEAMSAAHLAELKQKVLEHFAFIESE 259

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260 YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI+ F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320 RDICIDRVRMERDYFIENFLPAITDLEWVEKEVAKGRVWANALDRFRHAILEKQAELANM 379

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +T+  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380 ETETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560 NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 620 RQIEAKALRKLRHPTRSDRL 639


>gi|225076460|ref|ZP_03719659.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
            NRL30031/H210]
 gi|224952139|gb|EEG33348.1| hypothetical protein NEIFLAOT_01506 [Neisseria flavescens
            NRL30031/H210]
          Length = 650

 Score =  657 bits (1694), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/629 (54%), Positives = 451/629 (71%), Gaps = 23/629 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81   AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
             IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140  IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 1002 KGN----KNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFH 1043
             G+    K ++EE   +                    +S   L +LK + L  F+ I   
Sbjct: 200  LGHLENAKPDDEEGETVSDDEDGDDEDEDDSSSDSDAMSAAHLAELKQKVLEHFAFIESE 259

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260  YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FIK F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320  RDICIDRVRMDRDYFIKNFLPAITDLEWVEEEVAKGCVWANALDRFRHAILEKQTELANM 379

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380  EAETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560  NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            RQIEAKALRKLRHP+R  +L+ FL+ ++N
Sbjct: 620  RQIEAKALRKLRHPTRSDRLRSFLDSEEN 648



 Score =  640 bits (1650), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 336/620 (54%), Positives = 441/620 (71%), Gaps = 24/620 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D
Sbjct: 21  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            E ++LS+    +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 81  AEDILLSDNAAAMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 139

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
            IAK+IE  LK+M+ AIS+CP +I EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 140 IIAKKIENALKNMVQAISACPGSIAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 199

Query: 212 KGN----KNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFH 253
            G+    K ++EE   +                    +S   L +LK + L  F+ I   
Sbjct: 200 LGHLENAKPDDEEGETVSDDEDGDDEDEDDSSSDSDAMSAAHLAELKQKVLEHFAFIESE 259

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           + KM K  EK G    +Y+K  + I+N++L +RF  + IE L   LR+++  + ++E++I
Sbjct: 260 YGKMIKQLEKHGSQHANYLKHRDAIANKLLEVRFATRQIENLSSNLRSRVENIRKLEREI 319

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FIK F     +L WV+ E      +   L R   +I E Q +L N+
Sbjct: 320 RDICIDRVRMDRDYFIKNFLPAITDLEWVEEEVAKGCVWANALDRFRHAILEKQTELANM 379

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  + + +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380 EAETRISIEELKEINKNMVLSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 499

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 500 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDAN 559

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560 NVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 620 RQIEAKALRKLRHPTRSDRL 639


>gi|385203763|ref|ZP_10030633.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
 gi|385183654|gb|EIF32928.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. Ch1-1]
          Length = 665

 Score =  655 bits (1690), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/623 (52%), Positives = 444/623 (71%), Gaps = 20/623 (3%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44   QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 884  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 939
             D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104  PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 940  EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 999
            EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164  EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTIAAEED 223

Query: 1000 VIKGNKNNNEEKILIESS--------------SADLSTEQLEKLKYESLIKFSNISFHFD 1045
                + + + +                     +AD +  +L++L  + L  F+ +    D
Sbjct: 224  SASADASADVDADTDSDDDEDSDDDDGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282  QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342  IVVSKSGMPREKFIESFAGHEADLGWTERAARGASAYGAALERHLPAIQSEQQKLIEIEA 401

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402  TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462  IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522  ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582  SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IE+KA+RKL HPSR  +LK FL+
Sbjct: 642  IESKAMRKLMHPSRADRLKSFLD 664



 Score =  639 bits (1648), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 319/609 (52%), Positives = 434/609 (71%), Gaps = 20/609 (3%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E  +++ + LI+LGKE+GYLT ++IND LP++      I+SI+  F  M + V E  
Sbjct: 44  QQAEERQRQMRALIQLGKEQGYLTHAQINDHLPDNFAQTAAIDSIVSAFNDMGVQVYEQA 103

Query: 94  LDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDG 149
            D ETL+L++    + SDD  +E TE ALSTVDS+FGRT DP++MYMREMG+ ELLTR G
Sbjct: 104 PDAETLLLNSNAPAVVSDDQADEETEVALSTVDSEFGRTTDPVRMYMREMGATELLTRAG 163

Query: 150 EIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNR 209
           EI IAKRIE+GL +M+ AI++CP  I  IL +A +++  E++IDE+VDGL +   ++   
Sbjct: 164 EIAIAKRIEDGLHEMVQAIAACPLAISAILASAQQVADGELRIDELVDGLNEDTIAAEED 223

Query: 210 VIKGNKNNNEEKILIESS--------------SADLSTEQLEKLKYESLIKFSNISFHFD 255
               + + + +                     +AD +  +L++L  + L  F+ +    D
Sbjct: 224 SASADASADVDADTDSDDDEDSDDDDGPADSSAADEA--RLKQLTSDCLEIFAQVGMLSD 281

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +M  +  +    S++Y +A   I   +  IRFTA++I++LC  ++ Q+ QV  IE+ IL+
Sbjct: 282 QMNASHTRGDVTSKAYQRAREEIQQHLAKIRFTARTIDRLCGDVQQQVAQVRAIERNILQ 341

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K GMPR  FI+ F  +E +L W +   +    Y   L R++P+I+  QQKLI ++ 
Sbjct: 342 IVVSKSGMPREKFIESFAGHEADLGWTERAARGASAYGAALERHLPAIQSEQQKLIEIEA 401

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL  L++INR+M+A E K RKAK EM EANLRLVISIAKKY +RG+ FLDLIQEGN
Sbjct: 402 TVSLPLKHLKEINRQMVAAESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGN 461

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIR+PVHMIETINK++RISR+
Sbjct: 462 IGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRVPVHMIETINKLNRISRE 521

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           ILQ+TG E  PSV+A +ME+ EEK+R I+KIAK+PVSME+PVGDD D+ LGD IED    
Sbjct: 522 ILQQTGQEAHPSVLAERMELSEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAAS 581

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P+DAA+ A +R+ + D L+SL+PRE+KVLRMR+GI   SDHTLEEVGKQFDVTRERIRQ
Sbjct: 582 SPADAAMQADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQ 641

Query: 616 IEAKALRKL 624
           IE+KA+RKL
Sbjct: 642 IESKAMRKL 650


>gi|261377614|ref|ZP_05982187.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
 gi|269146367|gb|EEZ72785.1| RNA polymerase sigma factor RpoD [Neisseria cinerea ATCC 14685]
          Length = 642

 Score =  652 bits (1683), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 337/621 (54%), Positives = 447/621 (71%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHTPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSNADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILGLIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GNKNNNEEK-------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+  N   +                E  +  +S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLENTAHEEPANDDPDADEDDEESEGDADAISAANLAELKQKVIDHFAQIEKDYKKMIS 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + IE L   LR+++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL WV+ E      ++  L R   +I E Q +L N++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWVEEEVAKGRVWSDALDRFRHAILEKQTELANMERETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNIAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  638 bits (1645), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 334/614 (54%), Positives = 439/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHTPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSNADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILGLIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GNKNNNEEK-------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+  N   +                E  +  +S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLENTAHEEPANDDPDADEDDEESEGDADAISAANLAELKQKVIDHFAQIEKDYKKMIS 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + IE L   LR+++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL WV+ E      ++  L R   +I E Q +L N++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWVEEEVAKGRVWSDALDRFRHAILEKQTELANMERETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNIAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|72383848|ref|YP_293202.1| sigma-70 factor [Ralstonia eutropha JMP134]
 gi|72123191|gb|AAZ65345.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia eutropha JMP134]
          Length = 624

 Score =  652 bits (1683), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/616 (50%), Positives = 442/616 (71%), Gaps = 14/616 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  +++ + LI LG+ERGYLT ++IND LP++      +E+I+ TF  M ++V E   D 
Sbjct: 8    EERQRQMRALIALGRERGYLTHADINDHLPDNFTQTAAMETIVSTFSDMGVTVYEQAPDA 67

Query: 887  ETLMLSNIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL+LS+      SDD  +E  EAALSTVDS+FGRT DP+++YMREMG+ ELLTR GEIE
Sbjct: 68   DTLLLSDTAPAGASDDQADEEAEAALSTVDSEFGRTTDPVRLYMREMGASELLTRAGEIE 127

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK------NFSS 996
            IAKRIE GL+ MI AI++CP+ +  +L   D+I   E++IDE+V G+ D         +S
Sbjct: 128  IAKRIEGGLQGMIQAIAACPSVVSTMLADVDRIVAGELRIDELVYGISDDVNDSEIALAS 187

Query: 997  NNRVIKGNKNNNEE-KILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
            ++  ++ + ++++     +E  + D    +  +LE+L  +SL  F+ +   F+++  A  
Sbjct: 188  DDVHVEADASDDDPVGDDVEPDAGDSEKANAARLEQLTLDSLAIFARVRALFEQLPDAPV 247

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
                 S +  +  + I +E+  IRFTAK+I++LC ++  Q+ +V  IE+ ILEI V++CG
Sbjct: 248  TGKARSAAVEQLRSKIQSELAPIRFTAKTIDRLCASVHEQLTEVRAIERSILEIAVDRCG 307

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F++ FP NE +L W          +   L R++P+I+  QQKLI+++  + LPL 
Sbjct: 308  MPRKVFVESFPGNETDLKWTSKMAATSRQFGAALKRHLPAIQAGQQKLIDIEAKVTLPLQ 367

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
              + INR+M A E+K R+AKRE+ EANLRLVISIAKKY +RG+ FLDLIQEGNIGLMKAV
Sbjct: 368  QFKQINRQMSAAELKMRQAKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAV 427

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHM+E INK++RISR   Q+TG 
Sbjct: 428  DKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMVEMINKLNRISRDFRQQTGR 487

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            E  P+V+A +MEM EEK+R I++ A++PVS+E+PVGDD D+ LGD IED +  +P++AA+
Sbjct: 488  EAHPAVLAERMEMSEEKVRSILRSARQPVSLETPVGDDADATLGDMIEDVSASSPAEAAI 547

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            +A MR+ + + L+ L+PRE+KVLRMRFG++ +SD TLEEV KQFDVTRERIRQIE++A+R
Sbjct: 548  HADMRAAIDEALDGLSPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMR 607

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KL HPSR  KL+ FLE
Sbjct: 608  KLLHPSRADKLRPFLE 623



 Score =  635 bits (1638), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 304/602 (50%), Positives = 432/602 (71%), Gaps = 14/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  +++ + LI LG+ERGYLT ++IND LP++      +E+I+ TF  M ++V E   D 
Sbjct: 8   EERQRQMRALIALGRERGYLTHADINDHLPDNFTQTAAMETIVSTFSDMGVTVYEQAPDA 67

Query: 97  ETLMLSNIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL+LS+      SDD  +E  EAALSTVDS+FGRT DP+++YMREMG+ ELLTR GEIE
Sbjct: 68  DTLLLSDTAPAGASDDQADEEAEAALSTVDSEFGRTTDPVRLYMREMGASELLTRAGEIE 127

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK------NFSS 206
           IAKRIE GL+ MI AI++CP+ +  +L   D+I   E++IDE+V G+ D         +S
Sbjct: 128 IAKRIEGGLQGMIQAIAACPSVVSTMLADVDRIVAGELRIDELVYGISDDVNDSEIALAS 187

Query: 207 NNRVIKGNKNNNEE-KILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 262
           ++  ++ + ++++     +E  + D    +  +LE+L  +SL  F+ +   F+++  A  
Sbjct: 188 DDVHVEADASDDDPVGDDVEPDAGDSEKANAARLEQLTLDSLAIFARVRALFEQLPDAPV 247

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
                S +  +  + I +E+  IRFTAK+I++LC ++  Q+ +V  IE+ ILEI V++CG
Sbjct: 248 TGKARSAAVEQLRSKIQSELAPIRFTAKTIDRLCASVHEQLTEVRAIERSILEIAVDRCG 307

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F++ FP NE +L W          +   L R++P+I+  QQKLI+++  + LPL 
Sbjct: 308 MPRKVFVESFPGNETDLKWTSKMAATSRQFGAALKRHLPAIQAGQQKLIDIEAKVTLPLQ 367

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
             + INR+M A E+K R+AKRE+ EANLRLVISIAKKY +RG+ FLDLIQEGNIGLMKAV
Sbjct: 368 QFKQINRQMSAAELKMRQAKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAV 427

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRG+KFSTYATWW+RQA+TR++ADQARTIR+PVHM+E INK++RISR   Q+TG 
Sbjct: 428 DKFEYRRGWKFSTYATWWVRQAVTRALADQARTIRVPVHMVEMINKLNRISRDFRQQTGR 487

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           E  P+V+A +MEM EEK+R I++ A++PVS+E+PVGDD D+ LGD IED +  +P++AA+
Sbjct: 488 EAHPAVLAERMEMSEEKVRSILRSARQPVSLETPVGDDADATLGDMIEDVSASSPAEAAI 547

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           +A MR+ + + L+ L+PRE+KVLRMRFG++ +SD TLEEV KQFDVTRERIRQIE++A+R
Sbjct: 548 HADMRAAIDEALDGLSPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMR 607

Query: 623 KL 624
           KL
Sbjct: 608 KL 609


>gi|186472529|ref|YP_001859871.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia phymatum STM815]
 gi|184194861|gb|ACC72825.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum STM815]
          Length = 664

 Score =  652 bits (1682), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/620 (52%), Positives = 431/620 (69%), Gaps = 18/620 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  +++ + LI LG+ERGYLT ++IND LP++  +   +E+I+ TF  M +SV E   D 
Sbjct: 43   EERQRQMRALIALGRERGYLTHADINDHLPDNFTETAAMETIVSTFGEMGVSVYETAPDA 102

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            ETL+L    S   SDD  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR GEIE
Sbjct: 103  ETLLLNDGPSAAASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIE 162

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE GL+DM+ AI+ CP+ I  IL   D++   EI+IDE+VDG+ D   ++      
Sbjct: 163  IAKRIEGGLQDMVQAIAMCPSIIATILADVDRVVAGEIRIDELVDGISDTTEAAELDDDS 222

Query: 1003 GNKNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFHFDKMR 1048
                  EE     S                   +  +LE+L  +SL  F  +   F  + 
Sbjct: 223  AEAAAEEELETSASDDDSDDEDGDLSDDGGEKANAARLEQLTADSLAIFERVRALFASVP 282

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
                 +   + +      +I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+ IL+I V
Sbjct: 283  DMPVTDKRRATAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERSILQIAV 342

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            ++C MPR  F++ FP NE +L+W          Y   L R++P+I+  QQKL++++  I 
Sbjct: 343  DRCDMPRETFVESFPGNETDLDWTMRVAAKSKTYGPALERHLPAIQSEQQKLVDIEASIA 402

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            LPL  L+ IN+++ + E K R+AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIGL
Sbjct: 403  LPLQQLKQINKQLGSAESKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGL 462

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRG+KFSTYATWW+RQAITR+IADQARTIR+PVHMIE+INK++RI R+I+Q
Sbjct: 463  MKAVDKFEYRRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIVQ 522

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            +TG EP PSV+A +M+MPE KIR I+KIAK P S++SPVG+D D+ LGD IED +  +P+
Sbjct: 523  QTGQEPHPSVLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSPA 582

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA++A+MR  + + L++LTPRE+KVLRMR+GI+ +S+ TLEEVG+QFDVTRERIRQIE 
Sbjct: 583  DAAVHANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEG 642

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KA+RKL HPSR  KL+ FLE
Sbjct: 643  KAIRKLNHPSRADKLRPFLE 662



 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 314/606 (51%), Positives = 421/606 (69%), Gaps = 18/606 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  +++ + LI LG+ERGYLT ++IND LP++  +   +E+I+ TF  M +SV E   D 
Sbjct: 43  EERQRQMRALIALGRERGYLTHADINDHLPDNFTETAAMETIVSTFGEMGVSVYETAPDA 102

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           ETL+L    S   SDD  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR GEIE
Sbjct: 103 ETLLLNDGPSAAASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEIE 162

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE GL+DM+ AI+ CP+ I  IL   D++   EI+IDE+VDG+ D   ++      
Sbjct: 163 IAKRIEGGLQDMVQAIAMCPSIIATILADVDRVVAGEIRIDELVDGISDTTEAAELDDDS 222

Query: 213 GNKNNNEEKILIESSSAD--------------LSTEQLEKLKYESLIKFSNISFHFDKMR 258
                 EE     S                   +  +LE+L  +SL  F  +   F  + 
Sbjct: 223 AEAAAEEELETSASDDDSDDEDGDLSDDGGEKANAARLEQLTADSLAIFERVRALFASVP 282

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
                +   + +      +I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+ IL+I V
Sbjct: 283 DMPVTDKRRATAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERSILQIAV 342

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           ++C MPR  F++ FP NE +L+W          Y   L R++P+I+  QQKL++++  I 
Sbjct: 343 DRCDMPRETFVESFPGNETDLDWTMRVAAKSKTYGPALERHLPAIQSEQQKLVDIEASIA 402

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           LPL  L+ IN+++ + E K R+AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIGL
Sbjct: 403 LPLQQLKQINKQLGSAESKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGL 462

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRG+KFSTYATWW+RQAITR+IADQARTIR+PVHMIE+INK++RI R+I+Q
Sbjct: 463 MKAVDKFEYRRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIVQ 522

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           +TG EP PSV+A +M+MPE KIR I+KIAK P S++SPVG+D D+ LGD IED +  +P+
Sbjct: 523 QTGQEPHPSVLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSPA 582

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA++A+MR  + + L++LTPRE+KVLRMR+GI+ +S+ TLEEVG+QFDVTRERIRQIE 
Sbjct: 583 DAAVHANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEG 642

Query: 619 KALRKL 624
           KA+RKL
Sbjct: 643 KAIRKL 648


>gi|194289649|ref|YP_002005556.1| RNA polymerase sigma 70 (sigma d) factor [Cupriavidus taiwanensis LMG
            19424]
 gi|193223484|emb|CAQ69489.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus taiwanensis LMG
            19424]
          Length = 655

 Score =  651 bits (1680), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/617 (52%), Positives = 448/617 (72%), Gaps = 25/617 (4%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 41   QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVGTFAEMGVKIYEQTPDAETLL 100

Query: 891  LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            LS+   + SD+  EE  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 101  LSDGPVVASDEQAEEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 160

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            E+GL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +        + ++
Sbjct: 161  EDGLNNMVHAISACPFTIATILELSAKVASNEIGIDDVVDGLSDESIAEPAAAAADDADD 220

Query: 1008 NEEKILI-----------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
            +                       +S+ ADL+     +L+ E + +F+ ++  F++MR  
Sbjct: 221  SSLDSADETDEDDDDSADEGSSGQQSAEADLA-----RLREECMKRFARVAEQFERMRAE 275

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             E  G  + ++  A + +  E+  IRFTA++IE+LC  ++  +++V  IE+Q+++++V +
Sbjct: 276  SEAGGAATPAFAAARDAVREELRTIRFTARTIERLCANVQGMVDEVRAIERQVVQLLVER 335

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            CGM R   I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L 
Sbjct: 336  CGMEREDVIARFPGNETNLAWGQGLVAEDRPYSAAVARALPDLEAHQQKLIDIQARAALS 395

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L +L+ +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+QFLDLIQEGNIGLMK
Sbjct: 396  LAELKAVNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMQFLDLIQEGNIGLMK 455

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+T
Sbjct: 456  AVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQT 515

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EPDP+V+A +++M E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DA
Sbjct: 516  GKEPDPAVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADA 575

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            AL A +R+VV+++L+ L+PRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA
Sbjct: 576  ALQAGLRAVVREMLDELSPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKA 635

Query: 1411 LRKLRHPSRYYKLKIFL 1427
            ++KLRHPSR  +L  +L
Sbjct: 636  MKKLRHPSRADQLITYL 652



 Score =  638 bits (1646), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 440/605 (72%), Gaps = 25/605 (4%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           ++ + LI+LG++RGYLT ++I+D LPE+  D   +ESI+ TF  M + + E   D ETL+
Sbjct: 41  QQLRALIQLGRQRGYLTHADISDHLPENFTDTAAMESIVGTFAEMGVKIYEQTPDAETLL 100

Query: 101 LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           LS+   + SD+  EE  E AL+TVDS+FGRT DP++MYMREM S  LLTR  E+EIAKRI
Sbjct: 101 LSDGPVVASDEQAEEEAEVALATVDSEFGRTTDPVRMYMREMSSATLLTRKQEVEIAKRI 160

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           E+GL +M+HAIS+CP TI  IL  + K++ NEI ID++VDGL D++ +        + ++
Sbjct: 161 EDGLNNMVHAISACPFTIATILELSAKVASNEIGIDDVVDGLSDESIAEPAAAAADDADD 220

Query: 218 NEEKILI-----------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
           +                       +S+ ADL+     +L+ E + +F+ ++  F++MR  
Sbjct: 221 SSLDSADETDEDDDDSADEGSSGQQSAEADLA-----RLREECMKRFARVAEQFERMRAE 275

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            E  G  + ++  A + +  E+  IRFTA++IE+LC  ++  +++V  IE+Q+++++V +
Sbjct: 276 SEAGGAATPAFAAARDAVREELRTIRFTARTIERLCANVQGMVDEVRAIERQVVQLLVER 335

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
           CGM R   I  FP NE NL W          Y+  + R +P ++  QQKLI++Q    L 
Sbjct: 336 CGMEREDVIARFPGNETNLAWGQGLVAEDRPYSAAVARALPDLEAHQQKLIDIQARAALS 395

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L +L+ +NRKM+A E + R+AK EMT+ANLRLVISIAKKYT+RG+QFLDLIQEGNIGLMK
Sbjct: 396 LAELKAVNRKMLAAERQMRQAKHEMTQANLRLVISIAKKYTNRGMQFLDLIQEGNIGLMK 455

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIE INK++R+SR+I+Q+T
Sbjct: 456 AVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIEQINKLNRLSREIMQQT 515

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EPDP+V+A +++M E+K+R IMKIAKEPVSME+PVG+D D+ LGD I D +   P+DA
Sbjct: 516 GKEPDPAVLAERLDMTEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATPADA 575

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           AL A +R+VV+++L+ L+PRE+KVLRMRFGI+MS+D+TLEEVGKQFDVTRERIRQIE+KA
Sbjct: 576 ALQAGLRAVVREMLDELSPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKA 635

Query: 621 LRKLR 625
           ++KLR
Sbjct: 636 MKKLR 640


>gi|298369314|ref|ZP_06980632.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
            F0314]
 gi|298283317|gb|EFI24804.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 014 str.
            F0314]
          Length = 648

 Score =  651 bits (1679), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/629 (53%), Positives = 456/629 (72%), Gaps = 23/629 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 19   VEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 78

Query: 886  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             E ++LS+    IT DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 79   AEDILLSDNAATITDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 137

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
             IAK+IE  LK+M+ AIS+CP ++ EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 138  IIAKKIENALKNMVQAISACPGSVAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 197

Query: 1002 KGN------------------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
             G+                    +++++    + S  LS   LE+LK + L  F  I   
Sbjct: 198  LGHLENNASADDNNDSDNENDDESDDDEDDGNNDSDALSAANLEELKQKVLEHFVQIETA 257

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            + KM +   K      +Y++  + I++++L +RF  + IE L  +LRN+++ + ++E++I
Sbjct: 258  YTKMIEQLTKHHSRHAAYLEHRDAIASKLLEVRFATRQIESLSGSLRNRVDNIRKLEREI 317

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI+ F     +LNW++NE   ++ ++  L R   +I E Q +L  +
Sbjct: 318  RDICLDRVHMDRDYFIRNFLPVITDLNWLENEIAKENAWSGALDRFRHAILEKQTELAEM 377

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  + + +L+DIN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 378  EKETRISIGELKDINKNMVISEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 437

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 438  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 497

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 498  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDIN 557

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP+DAA+ +S+  V K++L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 558  NVAPADAAMYSSLHEVTKEVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 617

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            RQIEAKALRKLRHP+R  +L+ FL+ + N
Sbjct: 618  RQIEAKALRKLRHPTRSDRLRSFLDSEDN 646



 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 330/620 (53%), Positives = 447/620 (72%), Gaps = 24/620 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 19  VEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 78

Query: 96  TETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            E ++LS+    IT DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI
Sbjct: 79  AEDILLSDNAATITDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEI 137

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
            IAK+IE  LK+M+ AIS+CP ++ EIL   +++  +EI++DE+V+ +ID N    N + 
Sbjct: 138 IIAKKIENALKNMVQAISACPGSVAEILALIEQVRNDEIRVDEVVEAIIDPNEVLLNELG 197

Query: 212 KGN------------------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
            G+                    +++++    + S  LS   LE+LK + L  F  I   
Sbjct: 198 LGHLENNASADDNNDSDNENDDESDDDEDDGNNDSDALSAANLEELKQKVLEHFVQIETA 257

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           + KM +   K      +Y++  + I++++L +RF  + IE L  +LRN+++ + ++E++I
Sbjct: 258 YTKMIEQLTKHHSRHAAYLEHRDAIASKLLEVRFATRQIESLSGSLRNRVDNIRKLEREI 317

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI+ F     +LNW++NE   ++ ++  L R   +I E Q +L  +
Sbjct: 318 RDICLDRVHMDRDYFIRNFLPVITDLNWLENEIAKENAWSGALDRFRHAILEKQTELAEM 377

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  + + +L+DIN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 378 EKETRISIGELKDINKNMVISEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQE 437

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 438 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 497

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 498 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDIN 557

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP+DAA+ +S+  V K++L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 558 NVAPADAAMYSSLHEVTKEVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 617

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 618 RQIEAKALRKLRHPTRSDRL 637


>gi|390571824|ref|ZP_10252059.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia terrae BS001]
 gi|420247257|ref|ZP_14750668.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
 gi|389936240|gb|EIM98133.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia terrae BS001]
 gi|398071971|gb|EJL63211.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
          Length = 665

 Score =  650 bits (1676), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/621 (51%), Positives = 433/621 (69%), Gaps = 18/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  +++ + LI LG+ERGYLT ++IND LP++  +   +E+I+ TF  M +SV E   D
Sbjct: 43   VEERQRQMRALIALGRERGYLTHADINDHLPDNFTETAAMETIVSTFGEMGVSVYETAPD 102

Query: 886  TETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             ETL+L    S   SDD  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR GEI
Sbjct: 103  AETLLLNDGPSAAASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEI 162

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------- 991
            EIAKRIE GL+DM+ AI+ CP+ I  IL   D++   EI+IDE+VDG+ D          
Sbjct: 163  EIAKRIEGGLQDMVQAIAMCPSIISTILADVDRVVAGEIRIDELVDGISDTSEAAELDEE 222

Query: 992  ----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
                              ++ ++  L +      +  +LE+L  +SL  F  +   F  +
Sbjct: 223  AADAAAEEELEASASDEDSDEDDGDLSDDGGEKANAARLEQLTVDSLAIFGRVRDLFASV 282

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
                  +   + +      +I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+ IL+I 
Sbjct: 283  PDMPVTDKRRATAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERHILQIA 342

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V++C MPR  F++ FP NE +L+W          Y   L R++P+I+  QQKL++++  I
Sbjct: 343  VDRCDMPREAFVESFPGNETDLDWTMRIAAKSKSYGPALERHLPAIQSEQQKLVDIEASI 402

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             LPL  L+ IN+++ + E K R+AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIG
Sbjct: 403  ALPLQQLKQINKQLGSAEGKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIG 462

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRG+KFSTYATWW+RQAITR+IADQARTIR+PVHMIE+INK++RI R+I+
Sbjct: 463  LMKAVDKFEYRRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIV 522

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            Q+TG EP PSV+A +M+MPE KIR I+KIAK P S++SPVG+D D+ LGD IED +  +P
Sbjct: 523  QQTGQEPHPSVLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSP 582

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            +DAA++A+MR  + + L++LTPRE+KVLRMR+GI+ +S+ TLEEVG+QFDVTRERIRQIE
Sbjct: 583  ADAAVHANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIE 642

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
             KA+RKL HPSR  KL+ FLE
Sbjct: 643  GKAIRKLNHPSRADKLRPFLE 663



 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 423/607 (69%), Gaps = 18/607 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  +++ + LI LG+ERGYLT ++IND LP++  +   +E+I+ TF  M +SV E   D
Sbjct: 43  VEERQRQMRALIALGRERGYLTHADINDHLPDNFTETAAMETIVSTFGEMGVSVYETAPD 102

Query: 96  TETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            ETL+L    S   SDD  +E  E ALSTVDS+FGRT DP++MYMREMG+ ELLTR GEI
Sbjct: 103 AETLLLNDGPSAAASDDQADEEAEVALSTVDSEFGRTTDPVRMYMREMGASELLTRAGEI 162

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------- 201
           EIAKRIE GL+DM+ AI+ CP+ I  IL   D++   EI+IDE+VDG+ D          
Sbjct: 163 EIAKRIEGGLQDMVQAIAMCPSIISTILADVDRVVAGEIRIDELVDGISDTSEAAELDEE 222

Query: 202 ----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
                             ++ ++  L +      +  +LE+L  +SL  F  +   F  +
Sbjct: 223 AADAAAEEELEASASDEDSDEDDGDLSDDGGEKANAARLEQLTVDSLAIFGRVRDLFASV 282

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
                 +   + +      +I  E+  IRFTAK+I++LC  ++ Q+ QV  IE+ IL+I 
Sbjct: 283 PDMPVTDKRRATAIANLRESIQQELTPIRFTAKTIDRLCAEVQAQVAQVRAIERHILQIA 342

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V++C MPR  F++ FP NE +L+W          Y   L R++P+I+  QQKL++++  I
Sbjct: 343 VDRCDMPREAFVESFPGNETDLDWTMRIAAKSKSYGPALERHLPAIQSEQQKLVDIEASI 402

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            LPL  L+ IN+++ + E K R+AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIG
Sbjct: 403 ALPLQQLKQINKQLGSAEGKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIG 462

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRG+KFSTYATWW+RQAITR+IADQARTIR+PVHMIE+INK++RI R+I+
Sbjct: 463 LMKAVDKFEYRRGWKFSTYATWWVRQAITRAIADQARTIRVPVHMIESINKLNRIQREIV 522

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           Q+TG EP PSV+A +M+MPE KIR I+KIAK P S++SPVG+D D+ LGD IED +  +P
Sbjct: 523 QQTGQEPHPSVLAERMDMPEAKIRSILKIAKNPASLDSPVGEDADTTLGDMIEDTSATSP 582

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           +DAA++A+MR  + + L++LTPRE+KVLRMR+GI+ +S+ TLEEVG+QFDVTRERIRQIE
Sbjct: 583 ADAAVHANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIE 642

Query: 618 AKALRKL 624
            KA+RKL
Sbjct: 643 GKAIRKL 649


>gi|421563730|ref|ZP_16009546.1| RNA polymerase sigma factor [Neisseria meningitidis NM2795]
 gi|421907287|ref|ZP_16337169.1| RNA polymerase sigma factor rpoD Sigma-70 [Neisseria meningitidis
            alpha704]
 gi|393291626|emb|CCI73157.1| RNA polymerase sigma factor rpoD Sigma-70 [Neisseria meningitidis
            alpha704]
 gi|402340215|gb|EJU75418.1| RNA polymerase sigma factor [Neisseria meningitidis NM2795]
          Length = 642

 Score =  649 bits (1674), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/621 (53%), Positives = 451/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+VDS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSVDSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 332/614 (54%), Positives = 443/614 (72%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+VDS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSVDSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|1710686|sp|P52325.1|RPOD_NEIGO RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|808742|gb|AAA67115.1| sigma 70 [Neisseria gonorrhoeae]
          Length = 642

 Score =  648 bits (1672), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLRNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E  +  AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKVSAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  633 bits (1633), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLRNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E  +  AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKVSAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|254469018|ref|ZP_05082424.1| sigma 70 [beta proteobacterium KB13]
 gi|207087828|gb|EDZ65111.1| sigma 70 [beta proteobacterium KB13]
          Length = 658

 Score =  648 bits (1671), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/638 (55%), Positives = 439/638 (68%), Gaps = 33/638 (5%)

Query: 816  FDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 875
             D  SN +E  EN R + K LI LGKERGYLT +EIND LP++I + + ++ II     M
Sbjct: 30   LDEASNPKE-AENRRNQLKALIILGKERGYLTHAEINDHLPDEISETDQVDEIISIIHDM 88

Query: 876  DISVSEHVLDTETLMLSNI---TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSV 932
             I   +   D E L++ +     +D++  E  E AL+TVDS+FGRT DP++MYMREMG V
Sbjct: 89   GIRTYDEAPDAENLLMDDAPAPVTDEEAAEEAEQALATVDSEFGRTTDPVRMYMREMGKV 148

Query: 933  ELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK 992
             LL +  EIEIAKRIE+GLK M+ AIS+CP  I +++   DK+   E+ +DE VDGLID 
Sbjct: 149  GLLDKKEEIEIAKRIEDGLKHMVQAISACPGIIDDLMQMGDKVKAGELSVDEFVDGLID- 207

Query: 993  NFSSNNRVIKGNKNNNE-------------------EKILIESSSADLSTEQLEKLKYES 1033
                    ++  K  NE                   +      +   +S+E L+ L  E 
Sbjct: 208  --------LEAEKELNEALGMNDEESSNDEDSDDDDDDSSSSDNGKGMSSEDLKVLTEEV 259

Query: 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN-ISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            L +F  I     K+    EK  +  +   K H + I  E+L  RF+AK +E LCD +R  
Sbjct: 260  LKRFKKIKSAHKKLALLREKNKWIDDPEYKKHQDVIQKELLNFRFSAKLVEVLCDKVRQF 319

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            I Q+   E+ I++  VN+  MPR  FIK FP NE +  W+  E K    Y   L +   S
Sbjct: 320  IVQIRSHERTIMDFCVNQAKMPRTQFIKSFPGNETSNKWLKVEMKEDKPYIANLEKLKHS 379

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I + Q +L  L+    +P+ + ++INR+M  GE +AR+AKREM EANLRLVISIAKKYT+
Sbjct: 380  ILDQQAQLKELEDFSGIPIKNFKEINRQMTRGESRARRAKREMIEANLRLVISIAKKYTN 439

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 440  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 499

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQ TG EP+P+V+A KMEMPE+KIRKI+KI+KEP+SME+P+GDDED
Sbjct: 500  IETINKMNRISRQILQATGQEPEPAVLAEKMEMPEDKIRKILKISKEPISMETPIGDDED 559

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED   L P DAA+ +S+R+V  +IL  LTPRE+KVLRMRFGIEM++DHTLEEV
Sbjct: 560  SHLGDFIEDLGTLTPDDAAVYSSLRNVTNEILEGLTPREAKVLRMRFGIEMNTDHTLEEV 619

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            GKQFDVTRERIRQIEAKALRKLRHP+R  +LK FLEGK
Sbjct: 620  GKQFDVTRERIRQIEAKALRKLRHPTRSDRLKSFLEGK 657



 Score =  630 bits (1625), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 350/654 (53%), Positives = 441/654 (67%), Gaps = 36/654 (5%)

Query: 5   NKKTKIKNKKTKETLLKNA--FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIN 62
           N + K+  K+T++  +K       D  SN +E  EN R + K LI LGKERGYLT +EIN
Sbjct: 7   NPEEKVTPKRTRKPRVKKLKDLYLDEASNPKE-AENRRNQLKALIILGKERGYLTHAEIN 65

Query: 63  DFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI---TSDDDVEEATEAALS 119
           D LP++I + + ++ II     M I   +   D E L++ +     +D++  E  E AL+
Sbjct: 66  DHLPDEISETDQVDEIISIIHDMGIRTYDEAPDAENLLMDDAPAPVTDEEAAEEAEQALA 125

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           TVDS+FGRT DP++MYMREMG V LL +  EIEIAKRIE+GLK M+ AIS+CP  I +++
Sbjct: 126 TVDSEFGRTTDPVRMYMREMGKVGLLDKKEEIEIAKRIEDGLKHMVQAISACPGIIDDLM 185

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE-------------------E 220
              DK+   E+ +DE VDGLID         ++  K  NE                   +
Sbjct: 186 QMGDKVKAGELSVDEFVDGLID---------LEAEKELNEALGMNDEESSNDEDSDDDDD 236

Query: 221 KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN-IS 279
                 +   +S+E L+ L  E L +F  I     K+    EK  +  +   K H + I 
Sbjct: 237 DSSSSDNGKGMSSEDLKVLTEEVLKRFKKIKSAHKKLALLREKNKWIDDPEYKKHQDVIQ 296

Query: 280 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 339
            E+L  RF+AK +E LCD +R  I Q+   E+ I++  VN+  MPR  FIK FP NE + 
Sbjct: 297 KELLNFRFSAKLVEVLCDKVRQFIVQIRSHERTIMDFCVNQAKMPRTQFIKSFPGNETSN 356

Query: 340 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 399
            W+  E K    Y   L +   SI + Q +L  L+    +P+ + ++INR+M  GE +AR
Sbjct: 357 KWLKVEMKEDKPYIANLEKLKHSILDQQAQLKELEDFSGIPIKNFKEINRQMTRGESRAR 416

Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
           +AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 417 RAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 476

Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
           WIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ TG EP+P+V+A KMEMPE+K
Sbjct: 477 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQATGQEPEPAVLAEKMEMPEDK 536

Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
           IRKI+KI+KEP+SME+P+GDDEDSHLGDFIED   L P DAA+ +S+R+V  +IL  LTP
Sbjct: 537 IRKILKISKEPISMETPIGDDEDSHLGDFIEDLGTLTPDDAAVYSSLRNVTNEILEGLTP 596

Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 597 REAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRL 650


>gi|59801382|ref|YP_208094.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA 1090]
 gi|240014315|ref|ZP_04721228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI18]
 gi|240016750|ref|ZP_04723290.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA6140]
 gi|240121878|ref|ZP_04734840.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID24-1]
 gi|268681916|ref|ZP_06148778.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268684130|ref|ZP_06150992.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|293399243|ref|ZP_06643408.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
 gi|59718277|gb|AAW89682.1| putative RNA polymerase sigma factor [Neisseria gonorrhoeae FA 1090]
 gi|268622200|gb|EEZ54600.1| RNA polymerase sigma factor [Neisseria gonorrhoeae PID332]
 gi|268624414|gb|EEZ56814.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-92-679]
 gi|291610657|gb|EFF39767.1| RNA polymerase primary sigma factor [Neisseria gonorrhoeae F62]
          Length = 642

 Score =  648 bits (1671), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  633 bits (1633), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|194098357|ref|YP_002001415.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae NCCP11945]
 gi|254493553|ref|ZP_05106724.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268594613|ref|ZP_06128780.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268598759|ref|ZP_06132926.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268603436|ref|ZP_06137603.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|385335517|ref|YP_005889464.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae TCDC-NG08107]
 gi|193933647|gb|ACF29471.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512593|gb|EEH61938.1| RNA polymerase sigma factor rpoD [Neisseria gonorrhoeae 1291]
 gi|268548002|gb|EEZ43420.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|268582890|gb|EEZ47566.1| RNA polymerase sigma factor [Neisseria gonorrhoeae MS11]
 gi|268587567|gb|EEZ52243.1| sigma 70 domain-containing protein [Neisseria gonorrhoeae PID1]
 gi|317164060|gb|ADV07601.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 642

 Score =  647 bits (1670), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEVSAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  633 bits (1632), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEVSAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|268601118|ref|ZP_06135285.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291044060|ref|ZP_06569776.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 gi|268585249|gb|EEZ49925.1| RNA polymerase, sigma 70 subunit [Neisseria gonorrhoeae PID18]
 gi|291012523|gb|EFE04512.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
          Length = 642

 Score =  647 bits (1670), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSKDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  633 bits (1632), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSKDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|268686384|ref|ZP_06153246.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
 gi|268626668|gb|EEZ59068.1| RNA polymerase sigma factor [Neisseria gonorrhoeae SK-93-1035]
          Length = 642

 Score =  647 bits (1669), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENTLKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENTLKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|254672481|emb|CBA05947.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha275]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|313668077|ref|YP_004048361.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
 gi|313005539|emb|CBN86975.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|389605300|emb|CCA44220.1| RNA polymerase sigma factor rpoD Sigma-70 [Neisseria meningitidis
            alpha522]
          Length = 697

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 74   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 133

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 134  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 192

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 193  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 252

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 253  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 312

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 313  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 372

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 373  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 432

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 433  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 492

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 493  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 552

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 553  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 612

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 613  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 672

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 673  ALRKLRHPTRSDRLRSFLDSE 693



 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 335/635 (52%), Positives = 453/635 (71%), Gaps = 19/635 (2%)

Query: 16  KETLLKNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEI 74
           K+T+ +N    + + ++R   IE  R + + LI +GKERGY+T+SEIND LP+D+ D + 
Sbjct: 53  KQTMSRNQNHEEYQDDTRPLSIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 112

Query: 75  IESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDP 131
           I++I+     + I V+EH  D E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP
Sbjct: 113 IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDP 171

Query: 132 IKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIK 191
           ++MYMREMG V+LLTR+ EI IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI+
Sbjct: 172 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIR 231

Query: 192 IDEIVDGLIDKNFSSNNRVIKGN-KNNNEEK------------ILIESSSADLSTEQLEK 238
           +DE+V+ +ID N    N +  G+ +    EK               E  + ++S   L +
Sbjct: 232 VDEVVEAIIDPNEVLLNELGLGHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAE 291

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK + +  F+ I   + KM    EK     + Y+   + I+N++L +RF  + I+ L  +
Sbjct: 292 LKQKVIGHFAQIEKDYKKMIGRLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSS 351

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR ++  + ++E++I +I +++  M R +FI+ F     NL W++ E      ++  L R
Sbjct: 352 LRGKVENIRKLEREIRDICLDRVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDR 411

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
              +I E Q +L +++ +  + + +L++IN+ M++ E +   AK+EM +ANLRLVISIAK
Sbjct: 412 FRHAILEKQTELADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAK 471

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 472 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 531

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQ LQETG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+G
Sbjct: 532 PVHMIETINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIG 591

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHT
Sbjct: 592 DDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHT 651

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           LEEVG+QFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 652 LEEVGRQFDVTRERIRQIEAKALRKLRHPTRSDRL 686


>gi|15677390|ref|NP_274545.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|385323831|ref|YP_005878270.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
            8013]
 gi|385850892|ref|YP_005897407.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M04-240196]
 gi|385852857|ref|YP_005899371.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|416195944|ref|ZP_11617950.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis CU385]
 gi|416212636|ref|ZP_11621969.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240013]
 gi|418290972|ref|ZP_12903052.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NM220]
 gi|421538489|ref|ZP_15984665.1| RNA polymerase sigma factor [Neisseria meningitidis 93003]
 gi|421542828|ref|ZP_15988933.1| RNA polymerase sigma factor [Neisseria meningitidis NM255]
 gi|421551145|ref|ZP_15997145.1| RNA polymerase sigma factor [Neisseria meningitidis 69166]
 gi|421555182|ref|ZP_16001119.1| RNA polymerase sigma factor [Neisseria meningitidis 98008]
 gi|421556907|ref|ZP_16002817.1| RNA polymerase sigma factor [Neisseria meningitidis 80179]
 gi|421559492|ref|ZP_16005365.1| RNA polymerase sigma factor [Neisseria meningitidis 92045]
 gi|421566891|ref|ZP_16012632.1| RNA polymerase sigma factor [Neisseria meningitidis NM3001]
 gi|427826098|ref|ZP_18993159.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|433465520|ref|ZP_20422999.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM422]
 gi|433471713|ref|ZP_20429096.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 68094]
 gi|433477989|ref|ZP_20435306.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 70012]
 gi|433487869|ref|ZP_20445038.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M13255]
 gi|433490907|ref|ZP_20448026.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM418]
 gi|433505391|ref|ZP_20462329.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 9506]
 gi|433507532|ref|ZP_20464437.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 9757]
 gi|433522254|ref|ZP_20478940.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 61103]
 gi|433526469|ref|ZP_20483098.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 69096]
 gi|433539307|ref|ZP_20495781.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 70030]
 gi|7226783|gb|AAF41893.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 gi|261392218|emb|CAX49733.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
            8013]
 gi|316985995|gb|EFV64932.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325140674|gb|EGC63190.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis CU385]
 gi|325144806|gb|EGC67096.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240013]
 gi|325199861|gb|ADY95316.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis H44/76]
 gi|325205715|gb|ADZ01168.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M04-240196]
 gi|372200702|gb|EHP14737.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NM220]
 gi|402316516|gb|EJU52061.1| RNA polymerase sigma factor [Neisseria meningitidis 93003]
 gi|402316625|gb|EJU52168.1| RNA polymerase sigma factor [Neisseria meningitidis NM255]
 gi|402328679|gb|EJU64046.1| RNA polymerase sigma factor [Neisseria meningitidis 69166]
 gi|402331461|gb|EJU66798.1| RNA polymerase sigma factor [Neisseria meningitidis 98008]
 gi|402335291|gb|EJU70557.1| RNA polymerase sigma factor [Neisseria meningitidis 92045]
 gi|402336161|gb|EJU71423.1| RNA polymerase sigma factor [Neisseria meningitidis 80179]
 gi|402344834|gb|EJU79967.1| RNA polymerase sigma factor [Neisseria meningitidis NM3001]
 gi|432202175|gb|ELK58240.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM422]
 gi|432207670|gb|ELK63658.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 68094]
 gi|432214394|gb|ELK70295.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 70012]
 gi|432224900|gb|ELK80662.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M13255]
 gi|432226673|gb|ELK82399.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM418]
 gi|432240549|gb|ELK96084.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 9757]
 gi|432240683|gb|ELK96217.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 9506]
 gi|432258444|gb|ELL13728.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 61103]
 gi|432260229|gb|ELL15489.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 69096]
 gi|432272799|gb|ELL27905.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 70030]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|161870399|ref|YP_001599571.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 053442]
 gi|218768518|ref|YP_002343030.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis Z2491]
 gi|254805303|ref|YP_003083524.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis alpha14]
 gi|304387052|ref|ZP_07369304.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
            meningitidis ATCC 13091]
 gi|385328829|ref|YP_005883132.1| RNA polymerase sigma factor [Neisseria meningitidis alpha710]
 gi|385338353|ref|YP_005892226.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
            WUE 2594]
 gi|385855573|ref|YP_005902086.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240355]
 gi|416160524|ref|ZP_11606189.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis N1568]
 gi|416177216|ref|ZP_11609990.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M6190]
 gi|416182419|ref|ZP_11612045.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M13399]
 gi|416187009|ref|ZP_11614065.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M0579]
 gi|416191463|ref|ZP_11616089.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis ES14902]
 gi|418288695|ref|ZP_12901145.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NM233]
 gi|421561580|ref|ZP_16007421.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM2657]
 gi|421565905|ref|ZP_16011672.1| RNA polymerase sigma factor [Neisseria meningitidis NM3081]
 gi|433469720|ref|ZP_20427135.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 98080]
 gi|433473917|ref|ZP_20431276.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97021]
 gi|433475945|ref|ZP_20433282.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 88050]
 gi|433480027|ref|ZP_20437314.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63041]
 gi|433482427|ref|ZP_20439685.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2006087]
 gi|433484940|ref|ZP_20442154.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2002038]
 gi|433486735|ref|ZP_20443927.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97014]
 gi|433492927|ref|ZP_20450016.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM586]
 gi|433495052|ref|ZP_20452118.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM762]
 gi|433497221|ref|ZP_20454255.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M7089]
 gi|433499288|ref|ZP_20456295.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M7124]
 gi|433501253|ref|ZP_20458237.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM174]
 gi|433516031|ref|ZP_20472797.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2004090]
 gi|433517919|ref|ZP_20474662.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 96023]
 gi|433519238|ref|ZP_20475961.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 65014]
 gi|433524384|ref|ZP_20481042.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97020]
 gi|433528596|ref|ZP_20485204.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM3652]
 gi|433530803|ref|ZP_20487387.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM3642]
 gi|433533069|ref|ZP_20489629.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2007056]
 gi|433534877|ref|ZP_20491413.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2001212]
 gi|433537478|ref|ZP_20493973.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 77221]
 gi|433541383|ref|ZP_20497831.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63006]
 gi|121052526|emb|CAM08865.1| RNA polymerase sigma factor [Neisseria meningitidis Z2491]
 gi|161595952|gb|ABX73612.1| RNA polymerase primary sigma factor [Neisseria meningitidis 053442]
 gi|254668845|emb|CBA06900.1| RNA polymerase sigma factor [Neisseria meningitidis alpha14]
 gi|254669783|emb|CBA04064.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha153]
 gi|304338851|gb|EFM04953.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
            meningitidis ATCC 13091]
 gi|308389681|gb|ADO32001.1| RNA polymerase sigma factor [Neisseria meningitidis alpha710]
 gi|319410767|emb|CBY91151.1| RNA polymerase sigma factor RpoD (Sigma-70) [Neisseria meningitidis
            WUE 2594]
 gi|325128589|gb|EGC51459.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis N1568]
 gi|325132679|gb|EGC55363.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M6190]
 gi|325134647|gb|EGC57287.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M13399]
 gi|325136570|gb|EGC59171.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M0579]
 gi|325138535|gb|EGC61098.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis ES14902]
 gi|325204514|gb|ADY99967.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240355]
 gi|372201307|gb|EHP15249.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NM233]
 gi|402337280|gb|EJU72529.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM2657]
 gi|402342643|gb|EJU77802.1| RNA polymerase sigma factor [Neisseria meningitidis NM3081]
 gi|432202487|gb|ELK58550.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 98080]
 gi|432208846|gb|ELK64818.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97021]
 gi|432209054|gb|ELK65025.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 88050]
 gi|432214987|gb|ELK70878.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63041]
 gi|432215147|gb|ELK71037.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2006087]
 gi|432219177|gb|ELK75025.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2002038]
 gi|432221254|gb|ELK77067.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97014]
 gi|432227222|gb|ELK82933.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM586]
 gi|432229440|gb|ELK85128.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM762]
 gi|432232934|gb|ELK88569.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M7089]
 gi|432233715|gb|ELK89341.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis M7124]
 gi|432235059|gb|ELK90678.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM174]
 gi|432252357|gb|ELL07713.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2004090]
 gi|432252663|gb|ELL08015.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 96023]
 gi|432256166|gb|ELL11490.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 65014]
 gi|432258611|gb|ELL13892.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 97020]
 gi|432264275|gb|ELL19479.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM3652]
 gi|432265613|gb|ELL20805.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM3642]
 gi|432265812|gb|ELL21003.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2007056]
 gi|432270627|gb|ELL25763.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 2001212]
 gi|432271243|gb|ELL26369.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 77221]
 gi|432276924|gb|ELL31978.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63006]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|421546938|ref|ZP_15992979.1| RNA polymerase sigma factor [Neisseria meningitidis NM183]
 gi|421549188|ref|ZP_15995206.1| RNA polymerase sigma factor [Neisseria meningitidis NM2781]
 gi|421553118|ref|ZP_15999086.1| RNA polymerase sigma factor [Neisseria meningitidis NM576]
 gi|402322414|gb|EJU57876.1| RNA polymerase sigma factor [Neisseria meningitidis NM183]
 gi|402324578|gb|EJU60010.1| RNA polymerase sigma factor [Neisseria meningitidis NM2781]
 gi|402329028|gb|EJU64391.1| RNA polymerase sigma factor [Neisseria meningitidis NM576]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRRKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRRKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|385340414|ref|YP_005894286.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis G2136]
 gi|385341567|ref|YP_005895438.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240149]
 gi|385857586|ref|YP_005904098.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NZ-05/33]
 gi|416169328|ref|ZP_11608161.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis OX99.30304]
 gi|416202475|ref|ZP_11619975.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis 961-5945]
 gi|421540785|ref|ZP_15986924.1| RNA polymerase sigma factor [Neisseria meningitidis 93004]
 gi|433466577|ref|ZP_20424038.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 87255]
 gi|433502384|ref|ZP_20459354.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM126]
 gi|433509203|ref|ZP_20466075.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 12888]
 gi|433511739|ref|ZP_20468559.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 4119]
 gi|325130608|gb|EGC53353.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis OX99.30304]
 gi|325142722|gb|EGC65100.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis 961-5945]
 gi|325198658|gb|ADY94114.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis G2136]
 gi|325201773|gb|ADY97227.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis M01-240149]
 gi|325208475|gb|ADZ03927.1| RNA polymerase sigma factor rpoD [Neisseria meningitidis NZ-05/33]
 gi|402317823|gb|EJU53352.1| RNA polymerase sigma factor [Neisseria meningitidis 93004]
 gi|432204687|gb|ELK60726.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 87255]
 gi|432243058|gb|ELK98573.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis NM126]
 gi|432246386|gb|ELL01837.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 4119]
 gi|432247376|gb|ELL02814.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 12888]
          Length = 642

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|261400701|ref|ZP_05986826.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
 gi|269209456|gb|EEZ75911.1| RNA polymerase sigma factor RpoD [Neisseria lactamica ATCC 23970]
          Length = 642

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|121635207|ref|YP_975452.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis FAM18]
 gi|120866913|emb|CAM10672.1| RNA polymerase sigma factor [Neisseria meningitidis FAM18]
          Length = 658

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 35   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 94

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 95   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 153

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 154  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 213

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 214  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 273

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 274  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 333

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 334  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 393

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 394  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 453

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 454  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 513

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 514  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 573

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 574  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 633

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 634  ALRKLRHPTRSDRLRSFLDSE 654



 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 336/635 (52%), Positives = 453/635 (71%), Gaps = 19/635 (2%)

Query: 16  KETLLKNAFSFDIKSNSRE-EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEI 74
           K+T+ KN    + + ++R   IE  R + + LI +GKERGY+T+SEIND LP+D+ D + 
Sbjct: 14  KQTMSKNQNHEEYQDDARPLTIEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQ 73

Query: 75  IESIIKTFRYMDISVSEHVLDTETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDP 131
           I++I+     + I V+EH  D E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP
Sbjct: 74  IDNIVSMISGLGIQVTEHAPDAEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDP 132

Query: 132 IKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIK 191
           ++MYMREMG V+LLTR+ EI IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI+
Sbjct: 133 VRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIR 192

Query: 192 IDEIVDGLIDKNFSSNNRVIKGN-KNNNEEK------------ILIESSSADLSTEQLEK 238
           +DE+V+ +ID N    N +  G+ +    EK               E  + ++S   L +
Sbjct: 193 VDEVVEAIIDPNEVLLNELGLGHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAE 252

Query: 239 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 298
           LK + +  F+ I   + KM    EK     + Y+   + I+N++L +RF  + I+ L  +
Sbjct: 253 LKQKVIGHFAQIEKDYKKMIGRLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSS 312

Query: 299 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358
           LR ++  + ++E++I +I +++  M R +FI+ F     NL W++ E      ++  L R
Sbjct: 313 LRGKVENIRKLEREIRDICLDRVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDR 372

Query: 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 418
              +I E Q +L +++ +  + + +L++IN+ M++ E +   AK+EM +ANLRLVISIAK
Sbjct: 373 FRHAILEKQTELADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAK 432

Query: 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478
           KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 433 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 492

Query: 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538
           PVHMIETINK++RISRQ LQETG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+G
Sbjct: 493 PVHMIETINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIG 552

Query: 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598
           DD+DSHLGDFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHT
Sbjct: 553 DDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHT 612

Query: 599 LEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           LEEVG+QFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 613 LEEVGRQFDVTRERIRQIEAKALRKLRHPTRSDRL 647


>gi|422110508|ref|ZP_16380505.1| unnamed protein product [Neisseria lactamica Y92-1009]
 gi|309378741|emb|CBX22691.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 642

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 450/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDRFRHAILEKQTELADMERETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 442/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTVPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSDALDRFRHAILEKQTELADMERETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|319941927|ref|ZP_08016248.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319804580|gb|EFW01450.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 917

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/614 (54%), Positives = 436/614 (71%), Gaps = 11/614 (1%)

Query: 822  SREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE 881
            + E  E+ R K   LI LGKERGY+T+SEIND +P  ++D + IE+I+     ++I+V E
Sbjct: 312  AEESTEDRRSKLIKLISLGKERGYVTYSEINDNIPNTLLDEDAIETIVNILGNLNIAVHE 371

Query: 882  HVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
               D E L++   +   SD+D E   EAALSTV+S+FGRT DP+++YMREMGSVELL+R 
Sbjct: 372  VAPDEEQLLIQGGAEGVSDEDAEAEAEAALSTVESEFGRTTDPVRIYMREMGSVELLSRQ 431

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 998
             EIEI+KRIE+GLK M+ AI+ CP T+ EIL +A++I   E  IDE+VDG++  +   N 
Sbjct: 432  DEIEISKRIEDGLKHMVLAIARCPVTVHEILESAERIRSGETPIDEVVDGIVTPDDQKN- 490

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             V+   ++  +        ++ ++  QLE LK +SL  F  +  HF  + + F+ +G ++
Sbjct: 491  -VVGAVEDETD------MGASAMTVGQLEDLKEKSLAVFDRVEAHFRSLVETFDGKGPHA 543

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                   + I  E++ IRFTAK+ ++LC++LR  I  V   E+ + +  V    +PR  F
Sbjct: 544  PELEGLKDQIQRELMEIRFTAKTADRLCESLRRTIGIVRGSERTVYDEYVRHLHLPREWF 603

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +  F  N   + WVD       D   ++     +++E Q++L  L+ +  + + +L D  
Sbjct: 604  LANFISNATRIGWVDEVAAAYPDKAQVILHMRATVEEEQRRLAQLERESHMTVAELLDTY 663

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            ++M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDLIQEGN+GLMKAVDKFEYR
Sbjct: 664  KQMATGESKARNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYR 723

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN+++RI+RQ LQETG EPD   
Sbjct: 724  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINRMNRITRQELQETGVEPDSRR 783

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A  MEMPE+KI KIMKIAKEP+SME+P+GDD+DSHLGDF+ED   +AP++A  NAS+  
Sbjct: 784  LAELMEMPEDKILKIMKIAKEPISMETPIGDDDDSHLGDFLEDTQTVAPAEAVQNASLSD 843

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
             VK +L+SL+PRE+KVLRMRFGIEM SDHTLEEVGKQFDVTRERIRQIE KALRKLRHPS
Sbjct: 844  TVKQVLDSLSPREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQIETKALRKLRHPS 903

Query: 1419 RYYKLKIFLEGKKN 1432
            R  KLK FL+   N
Sbjct: 904  RADKLKSFLDETDN 917



 Score =  628 bits (1619), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 329/624 (52%), Positives = 435/624 (69%), Gaps = 16/624 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDF 64
           +KK++    K     +K+ +       + E  E+ R K   LI LGKERGY+T+SEIND 
Sbjct: 290 SKKSRAARDKALMEAMKHGYGA-----AEESTEDRRSKLIKLISLGKERGYVTYSEINDN 344

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTV 121
           +P  ++D + IE+I+     ++I+V E   D E L++   +   SD+D E   EAALSTV
Sbjct: 345 IPNTLLDEDAIETIVNILGNLNIAVHEVAPDEEQLLIQGGAEGVSDEDAEAEAEAALSTV 404

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           +S+FGRT DP+++YMREMGSVELL+R  EIEI+KRIE+GLK M+ AI+ CP T+ EIL +
Sbjct: 405 ESEFGRTTDPVRIYMREMGSVELLSRQDEIEISKRIEDGLKHMVLAIARCPVTVHEILES 464

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
           A++I   E  IDE+VDG++  +   N  V+   ++  +        ++ ++  QLE LK 
Sbjct: 465 AERIRSGETPIDEVVDGIVTPDDQKN--VVGAVEDETD------MGASAMTVGQLEDLKE 516

Query: 242 ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
           +SL  F  +  HF  + + F+ +G ++       + I  E++ IRFTAK+ ++LC++LR 
Sbjct: 517 KSLAVFDRVEAHFRSLVETFDGKGPHAPELEGLKDQIQRELMEIRFTAKTADRLCESLRR 576

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
            I  V   E+ + +  V    +PR  F+  F  N   + WVD       D   ++     
Sbjct: 577 TIGIVRGSERTVYDEYVRHLHLPREWFLANFISNATRIGWVDEVAAAYPDKAQVILHMRA 636

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
           +++E Q++L  L+ +  + + +L D  ++M  GE KAR AKREMTEANLRLVISIAKKYT
Sbjct: 637 TVEEEQRRLAQLERESHMTVAELLDTYKQMATGESKARNAKREMTEANLRLVISIAKKYT 696

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 697 NRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 756

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETIN+++RI+RQ LQETG EPD   +A  MEMPE+KI KIMKIAKEP+SME+P+GDD+
Sbjct: 757 MIETINRMNRITRQELQETGVEPDSRRLAELMEMPEDKILKIMKIAKEPISMETPIGDDD 816

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDF+ED   +AP++A  NAS+   VK +L+SL+PRE+KVLRMRFGIEM SDHTLEE
Sbjct: 817 DSHLGDFLEDTQTVAPAEAVQNASLSDTVKQVLDSLSPREAKVLRMRFGIEMQSDHTLEE 876

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIE KALRKLR
Sbjct: 877 VGKQFDVTRERIRQIETKALRKLR 900


>gi|325266676|ref|ZP_08133353.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
            denitrificans ATCC 33394]
 gi|324982119|gb|EGC17754.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella
            denitrificans ATCC 33394]
          Length = 671

 Score =  645 bits (1665), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 336/624 (53%), Positives = 451/624 (72%), Gaps = 20/624 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R++ + LI  GKERGY+T++EIND LP+D+ D E I+ ++   + + I V+E   D 
Sbjct: 45   EEQRERLRRLILQGKERGYITYAEINDALPDDMSDAEHIDGVVNMIQGLGIQVTEEAPDA 104

Query: 887  ETLMLSNITS---DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            +TL++S+ +S   D+D     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 105  DTLLMSDNSSAMTDEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 164

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IE  LK+MI AIS+CP ++ EIL   D++ K+EI++DE+V+ +ID N    N +  G
Sbjct: 165  AKEIENALKNMIQAISACPGSVGEILALIDQVKKDEIRVDEVVEAIIDPNEVLLNELGLG 224

Query: 1004 NKNNNE----------------EKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDK 1046
            +  NN                  +   ++ S  L ++Q LE+LK + L  F +I   +  
Sbjct: 225  HLENNSAHPAEESDGGEDDEDGGEDDEDADSGSLESQQNLEELKAQVLEHFKHIEKSYGL 284

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            M KA +K     ++Y+K  NNI+ ++L +RF+ + IE L + LR ++ Q+ ++E++I +I
Sbjct: 285  MVKALDKHHSKHDTYLKHRNNIAQKLLEVRFSTRQIENLSENLRGRVEQIRRLEREIRDI 344

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             +++  M R +FI+ F  N  NL W++ E      ++  L R    I E Q K+  L+  
Sbjct: 345  CLDRVRMDRDYFIEHFMPNATNLAWLEEEIGKNRVWSETLARFKHDILEKQAKMAELEAH 404

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              + + +L++I++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 405  ARISIAELKEISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 464

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ 
Sbjct: 465  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 524

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQETG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +A
Sbjct: 525  LQETGEEPDSAKLAELMDMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVA 584

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 585  PAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 644

Query: 1407 EAKALRKLRHPSRYYKLKIFLEGK 1430
            EAKALRKLRHP+R  KLK FL+ +
Sbjct: 645  EAKALRKLRHPTRSDKLKSFLDSE 668



 Score =  629 bits (1623), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 328/609 (53%), Positives = 440/609 (72%), Gaps = 20/609 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R++ + LI  GKERGY+T++EIND LP+D+ D E I+ ++   + + I V+E   D 
Sbjct: 45  EEQRERLRRLILQGKERGYITYAEINDALPDDMSDAEHIDGVVNMIQGLGIQVTEEAPDA 104

Query: 97  ETLMLSNITS---DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           +TL++S+ +S   D+D     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 105 DTLLMSDNSSAMTDEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 164

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IE  LK+MI AIS+CP ++ EIL   D++ K+EI++DE+V+ +ID N    N +  G
Sbjct: 165 AKEIENALKNMIQAISACPGSVGEILALIDQVKKDEIRVDEVVEAIIDPNEVLLNELGLG 224

Query: 214 NKNNNE----------------EKILIESSSADLSTEQ-LEKLKYESLIKFSNISFHFDK 256
           +  NN                  +   ++ S  L ++Q LE+LK + L  F +I   +  
Sbjct: 225 HLENNSAHPAEESDGGEDDEDGGEDDEDADSGSLESQQNLEELKAQVLEHFKHIEKSYGL 284

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           M KA +K     ++Y+K  NNI+ ++L +RF+ + IE L + LR ++ Q+ ++E++I +I
Sbjct: 285 MVKALDKHHSKHDTYLKHRNNIAQKLLEVRFSTRQIENLSENLRGRVEQIRRLEREIRDI 344

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            +++  M R +FI+ F  N  NL W++ E      ++  L R    I E Q K+  L+  
Sbjct: 345 CLDRVRMDRDYFIEHFMPNATNLAWLEEEIGKNRVWSETLARFKHDILEKQAKMAELEAH 404

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             + + +L++I++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 405 ARISIAELKEISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNI 464

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ 
Sbjct: 465 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQY 524

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQETG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +A
Sbjct: 525 LQETGEEPDSAKLAELMDMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVA 584

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 585 PAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 644

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 645 EAKALRKLR 653


>gi|404378126|ref|ZP_10983225.1| RNA polymerase sigma factor rpoD [Simonsiella muelleri ATCC 29453]
 gi|294483990|gb|EFG31673.1| RNA polymerase sigma factor rpoD [Simonsiella muelleri ATCC 29453]
          Length = 652

 Score =  645 bits (1664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 342/625 (54%), Positives = 452/625 (72%), Gaps = 21/625 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 28   EEQRARLRQLIIFGKERGYITYAEINDTLPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 87

Query: 887  ETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            ETL++S+     +D+D     EAALS  DS+FGRT DP++MYMREMG VELLTR  EI I
Sbjct: 88   ETLLMSDNSAAVADEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTRADEIII 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK+IE  LK+MI AIS+CP ++ EIL   D+I K+EI++DE+V+ +ID N    N +   
Sbjct: 148  AKKIENALKNMIQAISACPGSVGEILALIDQIKKDEIRVDEVVEAIIDPNEVLLNELGLS 207

Query: 1004 NKNNN---------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
            +  N                +E+   ++S ++L  + LE+LK + +  F  I   +  M 
Sbjct: 208  HLENGASEDDTSSESDDADDDEEDEEDASGSNLEGQNLEELKAQVIEHFKQIGKSYGLMI 267

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
            KA EK       Y++  + I++++L +RF+ + IEKL ++LR +++ + ++E++I +I +
Sbjct: 268  KALEKYDSKHTKYLEHRDAIASKLLEVRFSTRQIEKLSESLRGRVDLIRKLEREIRDICL 327

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            ++  M + +FI  F  N  NLNW+++E      ++  L R    I E Q ++ NL+    
Sbjct: 328  DRVRMDKDYFISSFLPNATNLNWIEDEINKNRVWSETLQRFKHDILEKQTEMSNLEAHAR 387

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            + + +L++I++ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 388  ISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 447

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQ
Sbjct: 448  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQ 507

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDDEDSHLGDFIED N +APS
Sbjct: 508  ETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDANNVAPS 567

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA+ +S+R V KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 568  DAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 627

Query: 1409 KALRKLRHPSRYYKLKIFL---EGK 1430
            KALRKLRHP+R  KLK FL   EGK
Sbjct: 628  KALRKLRHPTRSDKLKSFLDSEEGK 652



 Score =  629 bits (1621), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 331/607 (54%), Positives = 440/607 (72%), Gaps = 18/607 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 28  EEQRARLRQLIIFGKERGYITYAEINDTLPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 87

Query: 97  ETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           ETL++S+     +D+D     EAALS  DS+FGRT DP++MYMREMG VELLTR  EI I
Sbjct: 88  ETLLMSDNSAAVADEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTRADEIII 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK+IE  LK+MI AIS+CP ++ EIL   D+I K+EI++DE+V+ +ID N    N +   
Sbjct: 148 AKKIENALKNMIQAISACPGSVGEILALIDQIKKDEIRVDEVVEAIIDPNEVLLNELGLS 207

Query: 214 NKNNN---------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
           +  N                +E+   ++S ++L  + LE+LK + +  F  I   +  M 
Sbjct: 208 HLENGASEDDTSSESDDADDDEEDEEDASGSNLEGQNLEELKAQVIEHFKQIGKSYGLMI 267

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
           KA EK       Y++  + I++++L +RF+ + IEKL ++LR +++ + ++E++I +I +
Sbjct: 268 KALEKYDSKHTKYLEHRDAIASKLLEVRFSTRQIEKLSESLRGRVDLIRKLEREIRDICL 327

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           ++  M + +FI  F  N  NLNW+++E      ++  L R    I E Q ++ NL+    
Sbjct: 328 DRVRMDKDYFISSFLPNATNLNWIEDEINKNRVWSETLQRFKHDILEKQTEMSNLEAHAR 387

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           + + +L++I++ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 388 ISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 447

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQ
Sbjct: 448 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQ 507

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDDEDSHLGDFIED N +APS
Sbjct: 508 ETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDANNVAPS 567

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA+ +S+R V KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 568 DAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 627

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 628 KALRKLR 634


>gi|268597061|ref|ZP_06131228.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 gi|268550849|gb|EEZ45868.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
          Length = 642

 Score =  645 bits (1664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 333/621 (53%), Positives = 449/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
             A+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  VAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 618  ALRKLRHPTRSDRLRSFLDSE 638



 Score =  630 bits (1626), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 330/614 (53%), Positives = 441/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKICKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 CLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLQWIEEEIAKGRVWSNALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
            A+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 VAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 618 ALRKLRHPTRSDRL 631


>gi|238022360|ref|ZP_04602786.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
 gi|237866974|gb|EEP68016.1| hypothetical protein GCWU000324_02267 [Kingella oralis ATCC 51147]
          Length = 654

 Score =  645 bits (1663), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 339/630 (53%), Positives = 455/630 (72%), Gaps = 26/630 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R++ + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 25   EEQRERLRRLIIQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 84

Query: 887  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            ++L++   S   +D+D     EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI+I
Sbjct: 85   DSLLMNDNSTAITDEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVDLLTREDEIKI 144

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IE  LK+MI AIS+CP +I EIL   ++I K+EIK+DE+V+ +ID N    N +  G
Sbjct: 145  AKEIENALKNMIQAISACPGSIGEILDLINQIKKDEIKVDEVVEAIIDPNEVLLNELGLG 204

Query: 1004 NKNNN--------------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
            +  ++                     +    E  SA + ++ LE+LK + L  F  I   
Sbjct: 205  HLESSLNSHQAASGDESDESDGDESGDDDDSEGDSAAIESQNLEELKAQVLDHFKQIEKS 264

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            ++ M +A +K G +S  Y++   NI+N++L +RF+ + IEKL D+LR+++ ++ ++E++I
Sbjct: 265  YNLMIRALDKSGSSSAKYLEHRGNIANKLLEVRFSTRQIEKLSDSLRSRVEKIRKLEREI 324

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R HFI  F  N  NL+W++ E   +  ++  L R   +I E Q ++  L
Sbjct: 325  RDICLDRVNMDRDHFIAHFLPNATNLDWIEEEIAKKRAWSETLDRFRHAILEKQTEMAEL 384

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385  EQHARVSIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG +PD + +A  MEMPE+KIRKIMKIAKEP+SMESP+GDD+DSHLGDFIED N
Sbjct: 505  RQYLQETGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMESPIGDDDDSHLGDFIEDVN 564

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+ +S+R V   +L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565  NVAPAEAAMYSSLREVTAGVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFL---EGK 1430
            RQIEAKALRKLRHP+R  KLK FL   EGK
Sbjct: 625  RQIEAKALRKLRHPTRSDKLKSFLDSEEGK 654



 Score =  628 bits (1619), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 331/620 (53%), Positives = 446/620 (71%), Gaps = 24/620 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R++ + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 25  EEQRERLRRLIIQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 84

Query: 97  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           ++L++   S   +D+D     EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI+I
Sbjct: 85  DSLLMNDNSTAITDEDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVDLLTREDEIKI 144

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IE  LK+MI AIS+CP +I EIL   ++I K+EIK+DE+V+ +ID N    N +  G
Sbjct: 145 AKEIENALKNMIQAISACPGSIGEILDLINQIKKDEIKVDEVVEAIIDPNEVLLNELGLG 204

Query: 214 NKNNN--------------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
           +  ++                     +    E  SA + ++ LE+LK + L  F  I   
Sbjct: 205 HLESSLNSHQAASGDESDESDGDESGDDDDSEGDSAAIESQNLEELKAQVLDHFKQIEKS 264

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           ++ M +A +K G +S  Y++   NI+N++L +RF+ + IEKL D+LR+++ ++ ++E++I
Sbjct: 265 YNLMIRALDKSGSSSAKYLEHRGNIANKLLEVRFSTRQIEKLSDSLRSRVEKIRKLEREI 324

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R HFI  F  N  NL+W++ E   +  ++  L R   +I E Q ++  L
Sbjct: 325 RDICLDRVNMDRDHFIAHFLPNATNLDWIEEEIAKKRAWSETLDRFRHAILEKQTEMAEL 384

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385 EQHARVSIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG +PD + +A  MEMPE+KIRKIMKIAKEP+SMESP+GDD+DSHLGDFIED N
Sbjct: 505 RQYLQETGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMESPIGDDDDSHLGDFIEDVN 564

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+ +S+R V   +L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565 NVAPAEAAMYSSLREVTAGVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 625 RQIEAKALRKLRHPTRSDKL 644


>gi|421544853|ref|ZP_15990925.1| RNA polymerase sigma factor [Neisseria meningitidis NM140]
 gi|402322646|gb|EJU58098.1| RNA polymerase sigma factor [Neisseria meningitidis NM140]
          Length = 642

 Score =  644 bits (1661), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 333/621 (53%), Positives = 449/621 (72%), Gaps = 17/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRRKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALR LRHP+R  +L+ FL+ +
Sbjct: 618  ALRNLRHPTRSDRLRSFLDSE 638



 Score =  629 bits (1623), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 330/614 (53%), Positives = 441/614 (71%), Gaps = 18/614 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRRKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPAD 557

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 558 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 617

Query: 620 ALRKLR-PLAHDWL 632
           ALR LR P   D L
Sbjct: 618 ALRNLRHPTRSDRL 631


>gi|295701329|ref|YP_003610330.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
 gi|295441652|gb|ADG20819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. CCGE1002]
          Length = 663

 Score =  644 bits (1661), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 309/619 (49%), Positives = 438/619 (70%), Gaps = 17/619 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  +++ + LI+LGKERGYLT +EIND LP++      IE+I+ TF  M ++V E     
Sbjct: 44   EEQQRQMRALIQLGKERGYLTHAEINDHLPDNFAQTAAIETIVSTFNDMGVAVYEQAPSA 103

Query: 887  ETLMLSNITS----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            E L++++ T     DD  +E  E ALS+VDS+FGRT DP +MYMREMG+  LLTR GEIE
Sbjct: 104  EVLLMNDATPATMLDDQADEEAEVALSSVDSEFGRTTDPFRMYMREMGATGLLTRAGEIE 163

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS------- 995
            IAKRIE GL +M+ AI+  P T+  IL++A +I   E++IDE+VDG+  +  S       
Sbjct: 164  IAKRIEGGLHEMVQAIAVSPATVSAILLSAKQIEAGELRIDELVDGINAETESVEQSSTD 223

Query: 996  -----SNNRVIKGNKNNNEEKILIESSSADLSTE-QLEKLKYESLIKFSNISFHFDKMRK 1049
                    +    +    +E   IE      S E +L++L  +SL+ F+ +   F+++  
Sbjct: 224  FAEEPDTEQATADDDGGGDEHSEIEDRDTARSNEARLKQLTSDSLVIFARVRELFEQISG 283

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            +   +G    +       I  E+  IRFTA++I++LC+ ++ Q+ QV  +E+ IL+I V+
Sbjct: 284  SQAAQGKGRVARADLREAIQRELAPIRFTARTIDRLCNAVQQQVAQVRAVERHILQIAVD 343

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +CGMPR  F++ F   E +L W ++      +Y   L R++P+I+  Q+KL++++T + L
Sbjct: 344  RCGMPREKFVESFQGRETDLAWSESTAAASREYGAALERSLPAIQAEQRKLLDIETKVGL 403

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            PL  L+ INR+M+A E K  +AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIGLM
Sbjct: 404  PLQQLKKINRQMMAAESKMLQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLM 463

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIRIPVHM+E+INK++RISR+ILQ+
Sbjct: 464  KAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRIPVHMMESINKLNRISREILQQ 523

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG E  P+V+A +ME+PEEK+R ++KI ++P+S+E+PVGD+ D+ L D IED    +P+D
Sbjct: 524  TGREAHPAVLAQRMEVPEEKVRAMLKIGRQPLSLETPVGDEADTTLSDVIEDPMATSPAD 583

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+ A++R+ +   L++L+PRE+KVLRMRFGI+ +SD TLEE+GKQFD+TRERIRQIE+K
Sbjct: 584  AAVQANLRAAINTALDALSPREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESK 643

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            A+RKL HP+R  KL+ FL+
Sbjct: 644  AMRKLMHPNRTAKLRPFLD 662



 Score =  628 bits (1620), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 302/605 (49%), Positives = 428/605 (70%), Gaps = 17/605 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  +++ + LI+LGKERGYLT +EIND LP++      IE+I+ TF  M ++V E     
Sbjct: 44  EEQQRQMRALIQLGKERGYLTHAEINDHLPDNFAQTAAIETIVSTFNDMGVAVYEQAPSA 103

Query: 97  ETLMLSNITS----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           E L++++ T     DD  +E  E ALS+VDS+FGRT DP +MYMREMG+  LLTR GEIE
Sbjct: 104 EVLLMNDATPATMLDDQADEEAEVALSSVDSEFGRTTDPFRMYMREMGATGLLTRAGEIE 163

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS------- 205
           IAKRIE GL +M+ AI+  P T+  IL++A +I   E++IDE+VDG+  +  S       
Sbjct: 164 IAKRIEGGLHEMVQAIAVSPATVSAILLSAKQIEAGELRIDELVDGINAETESVEQSSTD 223

Query: 206 -----SNNRVIKGNKNNNEEKILIESSSADLSTE-QLEKLKYESLIKFSNISFHFDKMRK 259
                   +    +    +E   IE      S E +L++L  +SL+ F+ +   F+++  
Sbjct: 224 FAEEPDTEQATADDDGGGDEHSEIEDRDTARSNEARLKQLTSDSLVIFARVRELFEQISG 283

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
           +   +G    +       I  E+  IRFTA++I++LC+ ++ Q+ QV  +E+ IL+I V+
Sbjct: 284 SQAAQGKGRVARADLREAIQRELAPIRFTARTIDRLCNAVQQQVAQVRAVERHILQIAVD 343

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +CGMPR  F++ F   E +L W ++      +Y   L R++P+I+  Q+KL++++T + L
Sbjct: 344 RCGMPREKFVESFQGRETDLAWSESTAAASREYGAALERSLPAIQAEQRKLLDIETKVGL 403

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
           PL  L+ INR+M+A E K  +AKREM EANLRLVISIAKKY +RG+ FLDLIQEGNIGLM
Sbjct: 404 PLQQLKKINRQMMAAESKMLQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLM 463

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRG+KFSTYATWW+RQA+TRS+ADQARTIRIPVHM+E+INK++RISR+ILQ+
Sbjct: 464 KAVDKFEYRRGWKFSTYATWWVRQAVTRSLADQARTIRIPVHMMESINKLNRISREILQQ 523

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG E  P+V+A +ME+PEEK+R ++KI ++P+S+E+PVGD+ D+ L D IED    +P+D
Sbjct: 524 TGREAHPAVLAQRMEVPEEKVRAMLKIGRQPLSLETPVGDEADTTLSDVIEDPMATSPAD 583

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+ A++R+ +   L++L+PRE+KVLRMRFGI+ +SD TLEE+GKQFD+TRERIRQIE+K
Sbjct: 584 AAVQANLRAAINTALDALSPREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESK 643

Query: 620 ALRKL 624
           A+RKL
Sbjct: 644 AMRKL 648


>gi|329120411|ref|ZP_08249077.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
            bacilliformis ATCC BAA-1200]
 gi|327462095|gb|EGF08423.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
            bacilliformis ATCC BAA-1200]
          Length = 649

 Score =  642 bits (1657), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 332/628 (52%), Positives = 450/628 (71%), Gaps = 25/628 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R++ ++LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 23   EEQRQRLRLLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 82

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++    + +T DD VEEA EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 83   DTLLMNDTGTGMTDDDAVEEA-EAALSNADSEFGRTTDPVRMYMREMGQVDLLTREDEII 141

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------F 994
            IAK+IE  LK+MI AIS+CP +I EIL   +++   EIK+DE+V+ ++D N         
Sbjct: 142  IAKKIENALKNMIQAISACPGSIAEILGLIEQVRSGEIKVDEVVEAILDPNEVLMHELGV 201

Query: 995  SSNNRVIKGNKNNNE---------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
            S    +  G++ ++                +SS ++    LE+LK + L  F+ IS ++ 
Sbjct: 202  SDLEVIPPGSRPSDRAAEEENDEDGDEEDGASSEEIDRINLEELKQDVLAHFAGISENYG 261

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
             M +A + +G     Y+K  + I++++L +RF  + IE L  +LR +++ + ++E++I +
Sbjct: 262  LMVEALQAKGSKHPDYLKHRDAIAHKLLEVRFATRQIENLSGSLRQKVDNIRKLEREIRD 321

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            I +++  M R +FI  F  N  +L W++ E   +  +   L R   +I E Q ++  ++ 
Sbjct: 322  ICLDRVQMDRDYFIAQFLPNITDLGWLEGEIARRRVWGDALERFRHAILEKQTEVAEMEK 381

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               + + +L++IN+ M   E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 382  SAQISIEELKEINKNMQNSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGN 441

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 442  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 501

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQE G +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +
Sbjct: 502  YLQEHGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNV 561

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            AP++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 562  APAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 621

Query: 1406 IEAKALRKLRHPSRYYKLKIFL---EGK 1430
            IEAKALRKLRHP+R  +LK FL   EGK
Sbjct: 622  IEAKALRKLRHPTRSDRLKSFLDSEEGK 649



 Score =  626 bits (1615), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 325/618 (52%), Positives = 441/618 (71%), Gaps = 23/618 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R++ ++LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 23  EEQRQRLRLLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 82

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++    + +T DD VEEA EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 83  DTLLMNDTGTGMTDDDAVEEA-EAALSNADSEFGRTTDPVRMYMREMGQVDLLTREDEII 141

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------F 204
           IAK+IE  LK+MI AIS+CP +I EIL   +++   EIK+DE+V+ ++D N         
Sbjct: 142 IAKKIENALKNMIQAISACPGSIAEILGLIEQVRSGEIKVDEVVEAILDPNEVLMHELGV 201

Query: 205 SSNNRVIKGNKNNNE---------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
           S    +  G++ ++                +SS ++    LE+LK + L  F+ IS ++ 
Sbjct: 202 SDLEVIPPGSRPSDRAAEEENDEDGDEEDGASSEEIDRINLEELKQDVLAHFAGISENYG 261

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
            M +A + +G     Y+K  + I++++L +RF  + IE L  +LR +++ + ++E++I +
Sbjct: 262 LMVEALQAKGSKHPDYLKHRDAIAHKLLEVRFATRQIENLSGSLRQKVDNIRKLEREIRD 321

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           I +++  M R +FI  F  N  +L W++ E   +  +   L R   +I E Q ++  ++ 
Sbjct: 322 ICLDRVQMDRDYFIAQFLPNITDLGWLEGEIARRRVWGDALERFRHAILEKQTEVAEMEK 381

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              + + +L++IN+ M   E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 382 SAQISIEELKEINKNMQNSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGN 441

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 442 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 501

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQE G +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +
Sbjct: 502 YLQEHGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNV 561

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           AP++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 562 APAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 621

Query: 616 IEAKALRKLR-PLAHDWL 632
           IEAKALRKLR P   D L
Sbjct: 622 IEAKALRKLRHPTRSDRL 639


>gi|381401702|ref|ZP_09926595.1| RNA polymerase sigma factor RpoD [Kingella kingae PYKK081]
 gi|380833261|gb|EIC13136.1| RNA polymerase sigma factor RpoD [Kingella kingae PYKK081]
          Length = 654

 Score =  642 bits (1655), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/630 (54%), Positives = 449/630 (71%), Gaps = 26/630 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R++ + LI LGKERGY+T++EIND LP+D+ D E I+ I+   + + I V+E   D 
Sbjct: 25   EEQRERLRRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVTEEAPDA 84

Query: 887  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L++   S   +DDD     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 85   DALLMNDNSTGITDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 144

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IE  LK+MI AIS+CP ++ EIL   ++I K+EI++DE+V+ +ID N    N +  G
Sbjct: 145  AKEIENALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVVEAIIDPNEVLLNELGLG 204

Query: 1004 N-----KNNNEEKILIE--------------SSSADLSTEQ-LEKLKYESLIKFSNISFH 1043
            +     +++N+     +                +  +  +Q LE+LK E L  F  I   
Sbjct: 205  HLESSLQSDNDAATDSDDSSDESDEDDDSDSGDAGGMDNQQNLEELKAEVLEHFKQIEKS 264

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            +  M +A +K       Y++  NNI+ ++L +RF+ + IEKL D LR+++ Q+ ++E++I
Sbjct: 265  YGLMIRALDKNDSKHAKYLEHRNNIAQKLLEVRFSTRQIEKLSDNLRSRVEQIRKLEREI 324

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI+ F  N   L W+D E      ++  L R   +I E Q ++  L
Sbjct: 325  RDICLDRVRMDREYFIEQFMPNATYLEWIDEEVAKNRVWSEALGRFKHAILEKQTEMAAL 384

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385  EAHARISIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 505  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 564

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP+DAA+ +S+R V  DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565  NVAPADAAMYSSLREVTSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFL---EGK 1430
            RQIEAKALRKLRHP+R  KLK FL   EGK
Sbjct: 625  RQIEAKALRKLRHPTRSDKLKSFLDSEEGK 654



 Score =  625 bits (1611), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 333/620 (53%), Positives = 440/620 (70%), Gaps = 24/620 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R++ + LI LGKERGY+T++EIND LP+D+ D E I+ I+   + + I V+E   D 
Sbjct: 25  EEQRERLRRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVTEEAPDA 84

Query: 97  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L++   S   +DDD     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 85  DALLMNDNSTGITDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 144

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IE  LK+MI AIS+CP ++ EIL   ++I K+EI++DE+V+ +ID N    N +  G
Sbjct: 145 AKEIENALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVVEAIIDPNEVLLNELGLG 204

Query: 214 N-----KNNNEEKILIE--------------SSSADLSTEQ-LEKLKYESLIKFSNISFH 253
           +     +++N+     +                +  +  +Q LE+LK E L  F  I   
Sbjct: 205 HLESSLQSDNDAATDSDDSSDESDEDDDSDSGDAGGMDNQQNLEELKAEVLEHFKQIEKS 264

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           +  M +A +K       Y++  NNI+ ++L +RF+ + IEKL D LR+++ Q+ ++E++I
Sbjct: 265 YGLMIRALDKNDSKHAKYLEHRNNIAQKLLEVRFSTRQIEKLSDNLRSRVEQIRKLEREI 324

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI+ F  N   L W+D E      ++  L R   +I E Q ++  L
Sbjct: 325 RDICLDRVRMDREYFIEQFMPNATYLEWIDEEVAKNRVWSEALGRFKHAILEKQTEMAAL 384

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385 EAHARISIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 505 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 564

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP+DAA+ +S+R V  DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565 NVAPADAAMYSSLREVTSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 625 RQIEAKALRKLRHPTRSDKL 644


>gi|433513846|ref|ZP_20470634.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63049]
 gi|432246493|gb|ELL01940.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis 63049]
          Length = 641

 Score =  642 bits (1655), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/621 (53%), Positives = 449/621 (72%), Gaps = 18/621 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19   IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79   AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138  IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 1003 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
            G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198  GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258  RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318  RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378  SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
            TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD DSHLGDFIED N +AP+D
Sbjct: 498  TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDD-DSHLGDFIEDANNVAPAD 556

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 557  AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 616

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHP+R  +L+ FL+ +
Sbjct: 617  ALRKLRHPTRSDRLRSFLDSE 637



 Score =  627 bits (1617), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 331/614 (53%), Positives = 441/614 (71%), Gaps = 19/614 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           IE  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+EH  D
Sbjct: 19  IEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEHAPD 78

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+   +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 79  AEDILLSDNAAVTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   +KI K+EI++DE+V+ +ID N    N +  
Sbjct: 138 IAKKIENALKNMVQAISACPGSIAEILELIEKIRKDEIRVDEVVEAIIDPNEVLLNELGL 197

Query: 213 GN-KNNNEEK------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
           G+ +    EK               E  + ++S   L +LK + +  F+ I   + KM  
Sbjct: 198 GHLETTAPEKPSNDNSDENEDDEESEEDADEISAANLAELKQKVIGHFAQIEKDYKKMIG 257

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             EK     + Y+   + I+N++L +RF  + I+ L  +LR ++  + ++E++I +I ++
Sbjct: 258 RLEKHHSRHKDYLAYRDAIANKLLEVRFATRQIDSLSSSLRGKVENIRKLEREIRDICLD 317

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R +FI+ F     NL W++ E      ++  L R   +I E Q +L +++ +  +
Sbjct: 318 RVHMERDYFIQNFLPEITNLEWIEEEIAKGRVWSDALDRFRHAILEKQTELADMEKETRI 377

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 378 SIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 437

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE
Sbjct: 438 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQHLQE 497

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
           TG EPD + +A  M+MPE+KIRKIMKIAKEP+SME+P+GDD DSHLGDFIED N +AP+D
Sbjct: 498 TGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPIGDD-DSHLGDFIEDANNVAPAD 556

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           AA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAK
Sbjct: 557 AAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAK 616

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 617 ALRKLRHPTRSDRL 630


>gi|260222953|emb|CBA33035.1| RNA polymerase sigma factor rpoD [Curvibacter putative symbiont of
            Hydra magnipapillata]
          Length = 519

 Score =  640 bits (1652), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 315/515 (61%), Positives = 399/515 (77%), Gaps = 10/515 (1%)

Query: 922  IKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIK 981
            ++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ 
Sbjct: 1    MRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILRLGEEIREGKVV 60

Query: 982  IDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNIS 1041
            I  IVDG  + N + +    +     +E         +   T++LE+LK ++L +F  + 
Sbjct: 61   ITTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKMR 120

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              F+K+ K ++KEGY + +Y+KA   +S+E++ IRFTAK+IEKLCD +R Q++ V + E+
Sbjct: 121  ELFEKVHKVYDKEGYGTPAYVKAQKALSDELMTIRFTAKAIEKLCDMVRAQVDDVRKKER 180

Query: 1102 QILEIVVNKCGMPRLHFIKVF----------PENEINLNWVDNETKIQHDYNLILCRNIP 1151
            ++  I+V+KCG P+ +FI  F            N +NL W++ +      +  ++ RNIP
Sbjct: 181  ELRRIIVDKCGYPQENFIADFSGRDKAGNKVASNLLNLKWIEKQAASGKSWAAVMGRNIP 240

Query: 1152 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
             +++LQQKLI+LQ  +V+PL+ L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 241  PVQDLQQKLIDLQAQVVVPLDQLKDINKRMNEGEYASRAAKKEMIEANLRLVISIAKKYT 300

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 301  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 360

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINK++RISRQ LQE G EPD SV+A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 361  MIETINKMNRISRQHLQEFGFEPDASVLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDD 420

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 421  DSHLGDFIEDSANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEE 480

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            VGKQFDVTRERIRQIEAKALRKL+HPSR  KL+ F
Sbjct: 481  VGKQFDVTRERIRQIEAKALRKLKHPSRSDKLRSF 515



 Score =  626 bits (1614), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 308/504 (61%), Positives = 391/504 (77%), Gaps = 10/504 (1%)

Query: 132 IKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIK 191
           ++MYMREMG+VELLTR+GEIEIAKRIE GL DM+ AIS+ P TI EIL   ++I + ++ 
Sbjct: 1   MRMYMREMGTVELLTREGEIEIAKRIEGGLMDMMEAISASPATIAEILRLGEEIREGKVV 60

Query: 192 IDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNIS 251
           I  IVDG  + N + +    +     +E         +   T++LE+LK ++L +F  + 
Sbjct: 61  ITTIVDGFSNPNEADDYVAEEDFDEFDEADDDDGKGGSKALTKKLEELKKQALERFDKMR 120

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
             F+K+ K ++KEGY + +Y+KA   +S+E++ IRFTAK+IEKLCD +R Q++ V + E+
Sbjct: 121 ELFEKVHKVYDKEGYGTPAYVKAQKALSDELMTIRFTAKAIEKLCDMVRAQVDDVRKKER 180

Query: 312 QILEIVVNKCGMPRLHFIKVF----------PENEINLNWVDNETKIQHDYNLILCRNIP 361
           ++  I+V+KCG P+ +FI  F            N +NL W++ +      +  ++ RNIP
Sbjct: 181 ELRRIIVDKCGYPQENFIADFSGRDKAGNKVASNLLNLKWIEKQAASGKSWAAVMGRNIP 240

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            +++LQQKLI+LQ  +V+PL+ L+DIN++M  GE  +R AK+EM EANLRLVISIAKKYT
Sbjct: 241 PVQDLQQKLIDLQAQVVVPLDQLKDINKRMNEGEYASRAAKKEMIEANLRLVISIAKKYT 300

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 301 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 360

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ LQE G EPD SV+A KME+PE+KIRKIMKIAKEP+SME+P+GDD+
Sbjct: 361 MIETINKMNRISRQHLQEFGFEPDASVLAEKMEIPEDKIRKIMKIAKEPISMETPIGDDD 420

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED    AP +AA+ A +R VVKDIL+SLTPRE+KVLRMRFGIEM+SDHTLEE
Sbjct: 421 DSHLGDFIEDSANTAPMEAAMQAGLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEE 480

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKL+
Sbjct: 481 VGKQFDVTRERIRQIEAKALRKLK 504


>gi|333374621|ref|ZP_08466461.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae ATCC
            23330]
 gi|332975259|gb|EGK12159.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae ATCC
            23330]
          Length = 654

 Score =  637 bits (1643), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 341/630 (54%), Positives = 449/630 (71%), Gaps = 26/630 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R++ + LI LGKERGY+T++EIND LP+D+ D E I+ I+   + + I V+E   D 
Sbjct: 25   EEQRERLRRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVTEEAPDA 84

Query: 887  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L++   S   +DDD     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 85   DALLMNDNSTGITDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 144

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK IE  LK+MI AIS+CP ++ EIL   ++I K+EI++DE+V+ +ID N    N +  G
Sbjct: 145  AKEIENALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVVEAIIDPNEVLLNELGLG 204

Query: 1004 N-----KNNNEEKILIESSSADL---------------STEQLEKLKYESLIKFSNISFH 1043
            +     +++N+     + SS +                + + LE+LK E L  F  I   
Sbjct: 205  HLESSLQSDNDAATDSDDSSDESDEDDDSDSGDAGSMDNQQNLEELKAEVLEHFKQIEKS 264

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            +  M +  +K       Y++  NNI+ ++L +RF+ + IEKL D LR+++ Q+ ++E++I
Sbjct: 265  YGLMIRVLDKNDSKHAKYLEHRNNIAQKLLEVRFSTRQIEKLSDNLRSRVEQIRKLEREI 324

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI+ F  N   L W+D E      ++  L R   +I E Q ++  L
Sbjct: 325  RDICLDRVRMDREYFIEQFMPNATYLEWIDEEVAKNRVWSEALGRFKHAILEKQTEMAAL 384

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385  EAHARISIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 505  RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 564

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP+DAA+ +S+R V  DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565  NVAPADAAMYSSLREVTSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFL---EGK 1430
            RQIEAKALRKLRHP+R  KLK FL   EGK
Sbjct: 625  RQIEAKALRKLRHPTRSDKLKSFLDSEEGK 654



 Score =  620 bits (1599), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 333/620 (53%), Positives = 440/620 (70%), Gaps = 24/620 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R++ + LI LGKERGY+T++EIND LP+D+ D E I+ I+   + + I V+E   D 
Sbjct: 25  EEQRERLRRLIMLGKERGYITYAEINDSLPDDMSDAEQIDGIVNMIQSLGIQVTEEAPDA 84

Query: 97  ETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L++   S   +DDD     EAALS  DS+FGRT DP++MYMREMG VELLTR+ EI+I
Sbjct: 85  DALLMNDNSTGITDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVELLTREDEIKI 144

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK IE  LK+MI AIS+CP ++ EIL   ++I K+EI++DE+V+ +ID N    N +  G
Sbjct: 145 AKEIENALKNMIQAISACPGSVGEILELIEQIKKDEIRVDEVVEAIIDPNEVLLNELGLG 204

Query: 214 N-----KNNNEEKILIESSSADL---------------STEQLEKLKYESLIKFSNISFH 253
           +     +++N+     + SS +                + + LE+LK E L  F  I   
Sbjct: 205 HLESSLQSDNDAATDSDDSSDESDEDDDSDSGDAGSMDNQQNLEELKAEVLEHFKQIEKS 264

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           +  M +  +K       Y++  NNI+ ++L +RF+ + IEKL D LR+++ Q+ ++E++I
Sbjct: 265 YGLMIRVLDKNDSKHAKYLEHRNNIAQKLLEVRFSTRQIEKLSDNLRSRVEQIRKLEREI 324

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI+ F  N   L W+D E      ++  L R   +I E Q ++  L
Sbjct: 325 RDICLDRVRMDREYFIEQFMPNATYLEWIDEEVAKNRVWSEALGRFKHAILEKQTEMAAL 384

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +    + + +L+DI++ M+  E +   AK++M +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 385 EAHARISIAELKDISKNMVKSEKETAAAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQE 444

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 445 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 504

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 505 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 564

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP+DAA+ +S+R V  DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 565 NVAPADAAMYSSLREVTSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 624

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 625 RQIEAKALRKLRHPTRSDKL 644


>gi|225025101|ref|ZP_03714293.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC 23834]
 gi|224942062|gb|EEG23271.1| hypothetical protein EIKCOROL_01993 [Eikenella corrodens ATCC 23834]
          Length = 648

 Score =  634 bits (1635), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 333/625 (53%), Positives = 447/625 (71%), Gaps = 19/625 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+     + I V+E   D+
Sbjct: 22   EEQRARLRQLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMISGLGIQVTEETPDS 81

Query: 887  ETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            ETL++++ T++   DD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI I
Sbjct: 82   ETLLMADNTANMTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEIVI 141

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AK+IE  L++MI AIS+CP ++ EIL   +K+  +EI++DE+V+ +ID +    + +  G
Sbjct: 142  AKKIETALRNMIQAISACPGSVAEILELIEKVRNDEIRVDEVVEDIIDPHEELLDELGIG 201

Query: 1004 NKNNNEEK----------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
                 E                     E  +  +S   LE+LK + L  F +I   + KM
Sbjct: 202  VDKAEESAPEADLEESEDEDADEEDADEEDAGAISAANLEELKQKVLAHFEDIQATYKKM 261

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
              A +K     ++Y+   N I++++L +RFT + IE L + LR +++ + ++E++I +I 
Sbjct: 262  VAALQKHHSQHKTYLNLRNYIADQLLNVRFTTRQIETLSNNLRTRVDSIRRLEREIRDIC 321

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            +N+  M R +FI  F  N  +LNWV+ E      ++  L R   +I E Q  LI  +   
Sbjct: 322  LNRVHMDRDYFINNFLPNITDLNWVEAEIGKNRVWSEALSRFQYAIIEKQNILIEQEQHA 381

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             + + +L++I++ M+A E +   AKREM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 382  QISIAELKEISKNMVANEKETAAAKREMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 441

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ L
Sbjct: 442  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 501

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QETG +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP
Sbjct: 502  QETGEDPDAAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNIAP 561

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            +DAA+ +S+R   KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 562  ADAAMYSSLREATKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 1408 AKALRKLRHPSRYYKLKIFLEGKKN 1432
            AKALRKLRHP+R  +L+ FL+ ++N
Sbjct: 622  AKALRKLRHPTRSDRLRSFLDSEEN 646



 Score =  617 bits (1591), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 329/616 (53%), Positives = 437/616 (70%), Gaps = 20/616 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+     + I V+E   D+
Sbjct: 22  EEQRARLRQLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMISGLGIQVTEETPDS 81

Query: 97  ETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           ETL++++ T++   DD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI I
Sbjct: 82  ETLLMADNTANMTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEIVI 141

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AK+IE  L++MI AIS+CP ++ EIL   +K+  +EI++DE+V+ +ID +    + +  G
Sbjct: 142 AKKIETALRNMIQAISACPGSVAEILELIEKVRNDEIRVDEVVEDIIDPHEELLDELGIG 201

Query: 214 NKNNNEEK----------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
                E                     E  +  +S   LE+LK + L  F +I   + KM
Sbjct: 202 VDKAEESAPEADLEESEDEDADEEDADEEDAGAISAANLEELKQKVLAHFEDIQATYKKM 261

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
             A +K     ++Y+   N I++++L +RFT + IE L + LR +++ + ++E++I +I 
Sbjct: 262 VAALQKHHSQHKTYLNLRNYIADQLLNVRFTTRQIETLSNNLRTRVDSIRRLEREIRDIC 321

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           +N+  M R +FI  F  N  +LNWV+ E      ++  L R   +I E Q  LI  +   
Sbjct: 322 LNRVHMDRDYFINNFLPNITDLNWVEAEIGKNRVWSEALSRFQYAIIEKQNILIEQEQHA 381

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            + + +L++I++ M+A E +   AKREM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 382 QISIAELKEISKNMVANEKETAAAKREMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 441

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ L
Sbjct: 442 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 501

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QETG +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP
Sbjct: 502 QETGEDPDAAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNIAP 561

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           +DAA+ +S+R   KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 562 ADAAMYSSLREATKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 618 AKALRKLR-PLAHDWL 632
           AKALRKLR P   D L
Sbjct: 622 AKALRKLRHPTRSDRL 637


>gi|429744191|ref|ZP_19277698.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 020 str.
            F0370]
 gi|429163473|gb|EKY05693.1| RNA polymerase sigma factor RpoD [Neisseria sp. oral taxon 020 str.
            F0370]
          Length = 648

 Score =  633 bits (1632), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 338/630 (53%), Positives = 450/630 (71%), Gaps = 27/630 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 20   EEQRLRLRQLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 79

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++    + +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 80   DTLLMNDSGTGMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 138

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------F 994
            IAK+IE  LK+MI AIS+CP +I EIL   +KI  +EIK+D++V+ ++D N         
Sbjct: 139  IAKKIENALKNMIQAISACPGSIAEILDLIEKIRADEIKVDDVVEAILDPNEVLMHELGV 198

Query: 995  SSNNRVIKGNK-----------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
            S    +  G+K            + EE    ESS  +L +  LE+LK E L  FS I   
Sbjct: 199  SDLEIIPPGSKPSDRAAAAEEEGDGEEGDEDESSEENLESINLEELKQEVLAHFSGIGES 258

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            +  M  A  +       Y+K  + I++++L +RF  + IE L + LR +++ + ++E++I
Sbjct: 259  YGLMIAALNEHNSRHPDYLKHRDAIAHKLLEVRFATRQIESLSNNLRQKVDNIRKLEREI 318

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I +++  M R +FI  F  N  +L+W++ E   +  ++  L R   +I E Q ++  +
Sbjct: 319  RDICLDRVQMDRDYFISQFLPNITDLDWLEGEIGRKRVWSNALERFRHAILEKQTEVAEM 378

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            +    + + +L++I++ M + E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 379  EKTAQISIEELKEISKNMQSSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQE 438

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 439  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 498

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ LQE G +PD + +A  MEMPEEKIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 499  RQYLQEHGEDPDSAKLAELMEMPEEKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 558

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
             +AP++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 559  NVAPAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 618

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFL---EGK 1430
            RQIEAKALRKLRHP+R  +LK FL   EGK
Sbjct: 619  RQIEAKALRKLRHPTRSDRLKSFLDSEEGK 648



 Score =  617 bits (1590), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 331/620 (53%), Positives = 441/620 (71%), Gaps = 25/620 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + + LI  GKERGY+T++EIND LP+D+ D E I++I+   + + I V+E   D 
Sbjct: 20  EEQRLRLRQLILQGKERGYITYAEINDALPDDMSDAEQIDNIVNMIQGLGIQVTEEAPDA 79

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++    + +T DD VEEA EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 80  DTLLMNDSGTGMTDDDAVEEA-EAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 138

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------F 204
           IAK+IE  LK+MI AIS+CP +I EIL   +KI  +EIK+D++V+ ++D N         
Sbjct: 139 IAKKIENALKNMIQAISACPGSIAEILDLIEKIRADEIKVDDVVEAILDPNEVLMHELGV 198

Query: 205 SSNNRVIKGNK-----------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH 253
           S    +  G+K            + EE    ESS  +L +  LE+LK E L  FS I   
Sbjct: 199 SDLEIIPPGSKPSDRAAAAEEEGDGEEGDEDESSEENLESINLEELKQEVLAHFSGIGES 258

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           +  M  A  +       Y+K  + I++++L +RF  + IE L + LR +++ + ++E++I
Sbjct: 259 YGLMIAALNEHNSRHPDYLKHRDAIAHKLLEVRFATRQIESLSNNLRQKVDNIRKLEREI 318

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I +++  M R +FI  F  N  +L+W++ E   +  ++  L R   +I E Q ++  +
Sbjct: 319 RDICLDRVQMDRDYFISQFLPNITDLDWLEGEIGRKRVWSNALERFRHAILEKQTEVAEM 378

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           +    + + +L++I++ M + E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 379 EKTAQISIEELKEISKNMQSSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQE 438

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 439 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRIS 498

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ LQE G +PD + +A  MEMPEEKIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N
Sbjct: 499 RQYLQEHGEDPDSAKLAELMEMPEEKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVN 558

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
            +AP++AA+ +S+R V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 559 NVAPAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 618

Query: 614 RQIEAKALRKLR-PLAHDWL 632
           RQIEAKALRKLR P   D L
Sbjct: 619 RQIEAKALRKLRHPTRSDRL 638


>gi|345876372|ref|ZP_08828144.1| RNA polymerase sigma factor RpoD [Neisseria weaveri LMG 5135]
 gi|343966619|gb|EGV34874.1| RNA polymerase sigma factor RpoD [Neisseria weaveri LMG 5135]
          Length = 650

 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 340/648 (52%), Positives = 458/648 (70%), Gaps = 23/648 (3%)

Query: 808  FSKKNAFSFDIKSNSREEIENL-----RKKFKILIKLGKERGYLTFSEINDFLPEDIIDH 862
             S KN  S D   N +++   L     R + + LI +GKERGY+T+SEIND LP+D+ D 
Sbjct: 1    MSTKNTPSQDSDYNEQDDNRTLSPDEQRTRLRQLIIMGKERGYITYSEINDALPDDMSDA 60

Query: 863  EIIESIIKTFRYMDISVSEHVLDTETLMLSNITSD---DDVEEATEAALSTVDSDFGRTK 919
            E I++I+     + I V+E   D E ++LS+  +    DD     EAALS+VDS+FGRT 
Sbjct: 61   EQIDNIVSMISGLGIQVTEQAPDAEDILLSDNAAGMTDDDAVAEAEAALSSVDSEFGRTT 120

Query: 920  DPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNE 979
            DP++MYMREMG V+LLTR+ EI IAK+IE  LK+M+ AIS+CP +I +IL   +++  +E
Sbjct: 121  DPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMVQAISACPGSISDILELIERVRADE 180

Query: 980  IKIDEIVDGLIDKNFSSNNRVIKGNKNNN---------------EEKILIESSSADLSTE 1024
            IK+DE+V+ +ID N    N +  G+   +               +E+ + E+ +  +S  
Sbjct: 181  IKVDEVVEAIIDSNEVLLNELGLGHLEQSGGMENSEDPEDESDPDEEDVDEADAEAISAT 240

Query: 1025 QLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEK 1084
             LE+LK + L  F  I   +DKM    +K      SY+K  + I+ ++L +RF  + IE 
Sbjct: 241  NLEELKAKVLDHFEQIRTDYDKMVVQLKKHDSRHPSYLKHRDAIAAKLLEVRFATRQIEN 300

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNL 1144
            L  +LRN++  + ++E++I +I + +  M R +FI+ F  +  +L+WV+NE      ++ 
Sbjct: 301  LSSSLRNRVENIRKLEREIRDICLERVHMERDYFIQNFLPSITDLDWVNNEINKGRVWSN 360

Query: 1145 ILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVI 1204
             L R   +I E Q  L +++    + + +L++IN+ M+  E +   AK+EM +ANLRLVI
Sbjct: 361  ALDRFRHAIIEKQTFLSDMEKQAQISIEELKEINKNMVVSEKETSAAKQEMIQANLRLVI 420

Query: 1205 SIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 1264
            SIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR
Sbjct: 421  SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 480

Query: 1265 TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 1324
            TIRIPVHMIETINK++RISRQ LQE G EPD + +A  MEMPE+KIRKIMKIAKEP+SME
Sbjct: 481  TIRIPVHMIETINKMNRISRQYLQENGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISME 540

Query: 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMS 1384
            +P+GDD+DSHLGDFIED N +AP+DAA+ +S+R V KD+L SLTPRE+KVLRMRFGI+M+
Sbjct: 541  TPIGDDDDSHLGDFIEDINNVAPADAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMN 600

Query: 1385 SDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGKKN 1432
            +DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  +LK FL+ +++
Sbjct: 601  TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRLKSFLDSEEH 648



 Score =  614 bits (1584), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 329/612 (53%), Positives = 438/612 (71%), Gaps = 19/612 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           R + + LI +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D E +
Sbjct: 28  RTRLRQLIIMGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPDAEDI 87

Query: 100 MLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           +LS+  +    DD     EAALS+VDS+FGRT DP++MYMREMG V+LLTR+ EI IAK+
Sbjct: 88  LLSDNAAGMTDDDAVAEAEAALSSVDSEFGRTTDPVRMYMREMGQVDLLTREDEIIIAKK 147

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE  LK+M+ AIS+CP +I +IL   +++  +EIK+DE+V+ +ID N    N +  G+  
Sbjct: 148 IENALKNMVQAISACPGSISDILELIERVRADEIKVDEVVEAIIDSNEVLLNELGLGHLE 207

Query: 217 NN---------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
            +               +E+ + E+ +  +S   LE+LK + L  F  I   +DKM    
Sbjct: 208 QSGGMENSEDPEDESDPDEEDVDEADAEAISATNLEELKAKVLDHFEQIRTDYDKMVVQL 267

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           +K      SY+K  + I+ ++L +RF  + IE L  +LRN++  + ++E++I +I + + 
Sbjct: 268 KKHDSRHPSYLKHRDAIAAKLLEVRFATRQIENLSSSLRNRVENIRKLEREIRDICLERV 327

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            M R +FI+ F  +  +L+WV+NE      ++  L R   +I E Q  L +++    + +
Sbjct: 328 HMERDYFIQNFLPSITDLDWVNNEINKGRVWSNALDRFRHAIIEKQTFLSDMEKQAQISI 387

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            +L++IN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 388 EELKEINKNMVVSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 447

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G
Sbjct: 448 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQENG 507

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA
Sbjct: 508 EEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADAA 567

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
           + +S+R V KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 568 MYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 627

Query: 622 RKLR-PLAHDWL 632
           RKLR P   D L
Sbjct: 628 RKLRHPTRSDRL 639


>gi|254253609|ref|ZP_04946926.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898254|gb|EAY70097.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 773

 Score =  632 bits (1629), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 320/536 (59%), Positives = 406/536 (75%), Gaps = 26/536 (4%)

Query: 7   KTKIKNKKTKE-TLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFL 65
           K+K+++++ KE  LLK AF+      + EE+E  R K + LIKLGKERG+LT++EIND L
Sbjct: 151 KSKVRDRRAKEKALLKEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHL 209

Query: 66  PEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTV 121
           P++  + E +E II TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTV
Sbjct: 210 PDNFTETEALEGIIGTFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTV 269

Query: 122 DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIA 181
           DS+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  
Sbjct: 270 DSEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAM 329

Query: 182 ADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ------ 235
           A++++  EI++DE+VDGL+D N +  +    G      E I  E   A+   E+      
Sbjct: 330 AERVANEEIRVDELVDGLLDPNAADTD--TDGFSAKEAEAIENEDEDAEEEEEEEEEEDD 387

Query: 236 ------------LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
                       LE LK  SL KF+ IS  FDKMR+AFEKEGY S++Y+KA   I +E++
Sbjct: 388 DGAAQATANAAQLEALKRASLEKFALISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELM 447

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
            IRFTA+++E+LCDTLR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +
Sbjct: 448 TIRFTARTVERLCDTLRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAE 507

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
                 H Y+ +L RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKR
Sbjct: 508 KIAAEGHPYSAVLSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKR 567

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           EMTEANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 568 EMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 627

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
           AITRSIADQARTIRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE +
Sbjct: 628 AITRSIADQARTIRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPETR 683



 Score =  621 bits (1602), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 314/521 (60%), Positives = 394/521 (75%), Gaps = 25/521 (4%)

Query: 811  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 870
            K AF+      + EE+E  R K + LIKLGKERG+LT++EIND LP++  + E +E II 
Sbjct: 166  KEAFATSTPGTA-EELEERRVKLRALIKLGKERGFLTYAEINDHLPDNFTETEALEGIIG 224

Query: 871  TFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYM 926
            TF  M ++V E   D ETL+L++     +SDD+VEE  E ALSTVDS+FGRT DP++MYM
Sbjct: 225  TFNDMGVAVYEQAPDAETLLLNDNAPAASSDDEVEEEAEVALSTVDSEFGRTTDPVRMYM 284

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+VELLTR+GEIEIAKRIE+GL+ M+ AIS+CPTTI +IL  A++++  EI++DE+V
Sbjct: 285  REMGTVELLTREGEIEIAKRIEDGLRHMVMAISACPTTIADILAMAERVANEEIRVDELV 344

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ------------------LEK 1028
            DGL+D N +  +    G      E I  E   A+   E+                  LE 
Sbjct: 345  DGLLDPNAADTD--TDGFSAKEAEAIENEDEDAEEEEEEEEEEDDDGAAQATANAAQLEA 402

Query: 1029 LKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDT 1088
            LK  SL KF+ IS  FDKMR+AFEKEGY S++Y+KA   I +E++ IRFTA+++E+LCDT
Sbjct: 403  LKRASLEKFALISEWFDKMRRAFEKEGYKSKAYLKAQETIQSELMTIRFTARTVERLCDT 462

Query: 1089 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 1148
            LR Q+++V Q+E+QIL IVV+KCGMPR  FI  FP NE +L+W +      H Y+ +L R
Sbjct: 463  LRAQVDEVRQVERQILHIVVDKCGMPRSEFIARFPGNETDLDWAEKIAAEGHPYSAVLSR 522

Query: 1149 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK 1208
            NIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAK
Sbjct: 523  NIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAK 582

Query: 1209 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268
            KYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI
Sbjct: 583  KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 642

Query: 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 1309
            PVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE +
Sbjct: 643  PVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPETR 683


>gi|255066480|ref|ZP_05318335.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|340363135|ref|ZP_08685485.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria macacae
            ATCC 33926]
 gi|255049360|gb|EET44824.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|339886620|gb|EGQ76262.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria macacae
            ATCC 33926]
          Length = 649

 Score =  629 bits (1623), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 336/634 (52%), Positives = 445/634 (70%), Gaps = 38/634 (5%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21   LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81   AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141  IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 1003 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 1036
            G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201  GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252  FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312  RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            Q +L N++ +  + + +L+DIN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372  QTELANMEKETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492  NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552  DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            DVTRERIRQIEAKALRKLRHP+R  +L+ FL+ +
Sbjct: 612  DVTRERIRQIEAKALRKLRHPTRSDRLRSFLDSE 645



 Score =  615 bits (1585), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 333/627 (53%), Positives = 437/627 (69%), Gaps = 39/627 (6%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21  LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81  AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141 IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 213 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 246
           G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201 GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 306
           F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252 FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
            ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312 RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
           Q +L N++ +  + + +L+DIN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372 QTELANMEKETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552 DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 607 DVTRERIRQIEAKALRKLR-PLAHDWL 632
           DVTRERIRQIEAKALRKLR P   D L
Sbjct: 612 DVTRERIRQIEAKALRKLRHPTRSDRL 638


>gi|349573682|ref|ZP_08885656.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria shayeganii
            871]
 gi|348014736|gb|EGY53606.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria shayeganii
            871]
          Length = 648

 Score =  629 bits (1621), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 331/625 (52%), Positives = 448/625 (71%), Gaps = 19/625 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDI-IDHEIIESIIKTFRYMDISVSEHVLD 885
            E  R + + LI LGKERGY+T++EIND LP+++  D E I++II     + I V+E   D
Sbjct: 22   EEQRARLRQLILLGKERGYITYAEINDALPDEMSADAEQIDNIINMISGLGIQVTEEAPD 81

Query: 886  TETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E+L++ + T++   DD     EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 82   AESLLMGDNTANMTDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVDLLTREDEIV 141

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------- 991
            IAK+IE  L++MI AIS+CP ++ EIL   +KI K+E+++DE+V+ +ID           
Sbjct: 142  IAKKIETALRNMIQAISACPGSVAEILELVEKIRKDEVRVDEVVEDIIDPHEELLDELGI 201

Query: 992  ----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
                K  SS +  +  + + + +    ES S+ +S   LE+LK + L  F  I+  + KM
Sbjct: 202  GVAAKEDSSESADLDEDSDEDGDDDEEESDSSAISAANLEELKQKVLNHFEGIAGSYKKM 261

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
                +K      +Y+   + I++++  +RF  + IE L  +LR +++ + ++E++I +I 
Sbjct: 262  VAVLKKHDSRHANYLALRSEIADQLQNVRFATRQIEALSSSLRKRVDNIRRLEREIRDIC 321

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            +++  M R +FI  F     NL WV+ E   +  ++  L R   +I E Q +L +L+   
Sbjct: 322  LDRVHMDRDYFIASFLPQPTNLAWVEEEIAKKRVWSEALARFQYAIIEKQTELADLEKQA 381

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             + + +L++I++ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 382  QISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 441

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ L
Sbjct: 442  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 501

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QETG +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP
Sbjct: 502  QETGEDPDAAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAP 561

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            +DAA+ +S+R V +DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 562  ADAAMYSSLRDVTRDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 1408 AKALRKLRHPSRYYKLKIFLEGKKN 1432
            AKALRKLRHPSR  +LK FL+ ++ 
Sbjct: 622  AKALRKLRHPSRSDRLKSFLDSEEQ 646



 Score =  612 bits (1577), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 323/608 (53%), Positives = 436/608 (71%), Gaps = 19/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDI-IDHEIIESIIKTFRYMDISVSEHVLD 95
           E  R + + LI LGKERGY+T++EIND LP+++  D E I++II     + I V+E   D
Sbjct: 22  EEQRARLRQLILLGKERGYITYAEINDALPDEMSADAEQIDNIINMISGLGIQVTEEAPD 81

Query: 96  TETLMLSNITSD---DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E+L++ + T++   DD     EAALS  DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 82  AESLLMGDNTANMTDDDAVAEAEAALSQADSEFGRTTDPVRMYMREMGQVDLLTREDEIV 141

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------- 201
           IAK+IE  L++MI AIS+CP ++ EIL   +KI K+E+++DE+V+ +ID           
Sbjct: 142 IAKKIETALRNMIQAISACPGSVAEILELVEKIRKDEVRVDEVVEDIIDPHEELLDELGI 201

Query: 202 ----KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
               K  SS +  +  + + + +    ES S+ +S   LE+LK + L  F  I+  + KM
Sbjct: 202 GVAAKEDSSESADLDEDSDEDGDDDEEESDSSAISAANLEELKQKVLNHFEGIAGSYKKM 261

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
               +K      +Y+   + I++++  +RF  + IE L  +LR +++ + ++E++I +I 
Sbjct: 262 VAVLKKHDSRHANYLALRSEIADQLQNVRFATRQIEALSSSLRKRVDNIRRLEREIRDIC 321

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           +++  M R +FI  F     NL WV+ E   +  ++  L R   +I E Q +L +L+   
Sbjct: 322 LDRVHMDRDYFIASFLPQPTNLAWVEEEIAKKRVWSEALARFQYAIIEKQTELADLEKQA 381

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            + + +L++I++ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 382 QISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIG 441

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ L
Sbjct: 442 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYL 501

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QETG +PD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP
Sbjct: 502 QETGEDPDAAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAP 561

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           +DAA+ +S+R V +DIL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 562 ADAAMYSSLRDVTRDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 622 AKALRKLR 629


>gi|254447663|ref|ZP_05061129.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
            HTCC5015]
 gi|198263006|gb|EDY87285.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium
            HTCC5015]
          Length = 602

 Score =  629 bits (1621), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 325/605 (53%), Positives = 430/605 (71%), Gaps = 31/605 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP +I+D E +E II+    M I V E   D E L++
Sbjct: 20   QIKLLIAKGKEQGYLTFAEVNDHLPNEIVDPEQVEDIIQMINDMGIKVLESAPDAEELLM 79

Query: 892  --SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
               + ++D+D +EA  A L+  DSDFGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+
Sbjct: 80   MEGDTSNDEDADEAV-ANLANNDSDFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 138

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            GL+ ++ A+S+ P  +  +    D I + E +I +++ G ID +   ++ V   N   NE
Sbjct: 139  GLRQVVTALSTYPHAVNALFETYDGIIEREGRITDLIGGFIDPD---DDEVQNPNAPKNE 195

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-----EG-YNSESYIK 1063
            ++   E +  DL                  ++ H ++MRK +EK     +G Y  E+  K
Sbjct: 196  DEEAEEDTGPDLE----------------EVAKHINQMRKQYEKATKKKDGIYQREA--K 237

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   +S   + ++     I +    +R+ + +V Q+E+ ++ I V++CGMPR  FI  FP
Sbjct: 238  ASEKLSELFMQLKLDNNFINREIQLVRDVVGRVRQLERDVMTICVHRCGMPRKTFIDSFP 297

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
            ENE N NWV + +K +  +   +  +   + ELQQ LI ++ +  L ++DL++INRKM  
Sbjct: 298  ENETNPNWVKDHSKSKK-FGEKIAAHANDLNELQQHLIRIEQESGLSISDLKEINRKMSI 356

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            G+ KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 357  GQAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 416

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M
Sbjct: 417  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERM 476

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+K+RK++KIAKEP+SME+PVGDDEDS LGDF++D N  +P +AA+   +    +DI
Sbjct: 477  EMPEDKVRKVLKIAKEPISMETPVGDDEDSSLGDFLQDVNAESPIEAAVGEGLSESTRDI 536

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 537  LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDSL 596

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 597  RSFLD 601



 Score =  615 bits (1586), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 322/600 (53%), Positives = 424/600 (70%), Gaps = 32/600 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP +I+D E +E II+    M I V E   D E L++
Sbjct: 20  QIKLLIAKGKEQGYLTFAEVNDHLPNEIVDPEQVEDIIQMINDMGIKVLESAPDAEELLM 79

Query: 102 --SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
              + ++D+D +EA  A L+  DSDFGRT DP++MYMREMG+VELLTR+GEIEIAKRIE+
Sbjct: 80  MEGDTSNDEDADEAV-ANLANNDSDFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIED 138

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           GL+ ++ A+S+ P  +  +    D I + E +I +++ G ID +   ++ V   N   NE
Sbjct: 139 GLRQVVTALSTYPHAVNALFETYDGIIEREGRITDLIGGFIDPD---DDEVQNPNAPKNE 195

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-----EG-YNSESYIK 273
           ++   E +  DL                  ++ H ++MRK +EK     +G Y  E+  K
Sbjct: 196 DEEAEEDTGPDLE----------------EVAKHINQMRKQYEKATKKKDGIYQREA--K 237

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   +S   + ++     I +    +R+ + +V Q+E+ ++ I V++CGMPR  FI  FP
Sbjct: 238 ASEKLSELFMQLKLDNNFINREIQLVRDVVGRVRQLERDVMTICVHRCGMPRKTFIDSFP 297

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
           ENE N NWV + +K +  +   +  +   + ELQQ LI ++ +  L ++DL++INRKM  
Sbjct: 298 ENETNPNWVKDHSKSKK-FGEKIAAHANDLNELQQHLIRIEQESGLSISDLKEINRKMSI 356

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           G+ KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 357 GQAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 416

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M
Sbjct: 417 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERM 476

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+K+RK++KIAKEP+SME+PVGDDEDS LGDF++D N  +P +AA+   +    +DI
Sbjct: 477 EMPEDKVRKVLKIAKEPISMETPVGDDEDSSLGDFLQDVNAESPIEAAVGEGLSESTRDI 536

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 537 LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDSL 596


>gi|349610018|ref|ZP_08889380.1| RNA polymerase sigma factor rpoD [Neisseria sp. GT4A_CT1]
 gi|348610788|gb|EGY60470.1| RNA polymerase sigma factor rpoD [Neisseria sp. GT4A_CT1]
          Length = 649

 Score =  628 bits (1620), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 336/634 (52%), Positives = 444/634 (70%), Gaps = 38/634 (5%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21   LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81   AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141  IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 1003 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 1036
            G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201  GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252  FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312  RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            Q +L N++ +  + + +L+DIN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372  QTELANMEKETRISIEELKDINKNMVLSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492  NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552  DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            DVTRERIRQIEAKALRKLRHP+R  +L+ FL+ +
Sbjct: 612  DVTRERIRQIEAKALRKLRHPTRSDRLRSFLDSE 645



 Score =  613 bits (1582), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 333/627 (53%), Positives = 436/627 (69%), Gaps = 39/627 (6%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21  LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81  AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141 IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 213 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 246
           G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201 GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 306
           F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252 FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
            ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312 RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
           Q +L N++ +  + + +L+DIN+ M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372 QTELANMEKETRISIEELKDINKNMVLSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552 DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 607 DVTRERIRQIEAKALRKLR-PLAHDWL 632
           DVTRERIRQIEAKALRKLR P   D L
Sbjct: 612 DVTRERIRQIEAKALRKLRHPTRSDRL 638


>gi|261363710|ref|ZP_05976593.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
 gi|288568271|gb|EFC89831.1| RNA polymerase sigma factor RpoD [Neisseria mucosa ATCC 25996]
          Length = 649

 Score =  628 bits (1619), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 334/625 (53%), Positives = 447/625 (71%), Gaps = 20/625 (3%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21   LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81   AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141  IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 1003 GN-----------------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
            G+                 ++ +E+     S +  +S   L +LK + L  F+ I   + 
Sbjct: 201  GHLESASNDDDSGSSDEDEEDEDEDDDDSGSDAEAMSAAHLAELKQKVLDHFAFIESEYG 260

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            KM K  EK   +   Y+   + I+N++L +RF  + IE L   LR+++  + ++E++I +
Sbjct: 261  KMIKKLEKHDSSHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRD 320

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E Q +L N++ 
Sbjct: 321  ICLDRAHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEKQTELANMEK 380

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
            +  + + +L+DIN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 381  ETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGN 440

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 441  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 500

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +
Sbjct: 501  YLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNV 560

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 561  APADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 620

Query: 1406 IEAKALRKLRHPSRYYKLKIFLEGK 1430
            IEAKALRKLRHP+R  +L+ FL+ +
Sbjct: 621  IEAKALRKLRHPTRSDRLRSFLDSE 645



 Score =  613 bits (1581), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 331/618 (53%), Positives = 439/618 (71%), Gaps = 21/618 (3%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21  LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81  AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141 IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 213 GN-----------------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
           G+                 ++ +E+     S +  +S   L +LK + L  F+ I   + 
Sbjct: 201 GHLESASNDDDSGSSDEDEEDEDEDDDDSGSDAEAMSAAHLAELKQKVLDHFAFIESEYG 260

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           KM K  EK   +   Y+   + I+N++L +RF  + IE L   LR+++  + ++E++I +
Sbjct: 261 KMIKKLEKHDSSHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENIRKLEREIRD 320

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E Q +L N++ 
Sbjct: 321 ICLDRAHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEKQTELANMEK 380

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
           +  + + +L+DIN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 381 ETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGN 440

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 441 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQ 500

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +
Sbjct: 501 YLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNV 560

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 561 APADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 620

Query: 616 IEAKALRKLR-PLAHDWL 632
           IEAKALRKLR P   D L
Sbjct: 621 IEAKALRKLRHPTRSDRL 638


>gi|419796866|ref|ZP_14322382.1| RNA polymerase sigma factor RpoD [Neisseria sicca VK64]
 gi|385699057|gb|EIG29378.1| RNA polymerase sigma factor RpoD [Neisseria sicca VK64]
          Length = 649

 Score =  627 bits (1617), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 335/634 (52%), Positives = 445/634 (70%), Gaps = 38/634 (5%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21   LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 886  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
             E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81   AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141  IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 1003 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 1036
            G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201  GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252  FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312  RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            Q +L N++ +  + + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372  QTELANMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492  NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552  DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            DVTRERIRQIEAKALRKLRHP+R  +L+ FL+ +
Sbjct: 612  DVTRERIRQIEAKALRKLRHPTRSDRLRSFLDSE 645



 Score =  612 bits (1579), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 332/627 (52%), Positives = 437/627 (69%), Gaps = 39/627 (6%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E  R + + LI +GKERGY+T+SEIND LP+D+ D + I++I+     + I V+E   D
Sbjct: 21  LEEQRARLRQLIIMGKERGYITYSEINDALPDDMSDADQIDNIVSMISGLGIQVTEQAPD 80

Query: 96  TETLMLSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
            E ++LS+     +DDD     EAALS+ DS+FGRT DP++MYMREMG V+LLTR+ EI 
Sbjct: 81  AEDILLSDNAAAVTDDDAVAEAEAALSSADSEFGRTTDPVRMYMREMGQVDLLTREDEII 140

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAK+IE  LK+M+ AIS+CP +I EIL   ++I K+EI++DE+V+ +ID N    N +  
Sbjct: 141 IAKKIENALKNMVQAISACPGSIAEILELIEQIRKDEIRVDEVVEAIIDPNEVLLNELGL 200

Query: 213 GNKNNNEEKILIESSSAD--------------------------LSTEQLEKLKYESLIK 246
           G+         +ES+S D                          +S   L +LK + L  
Sbjct: 201 GH---------LESASNDDDSGSSEEDEADEDDDDDDSGSDSEAMSAAHLAELKQKVLEH 251

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 306
           F+ I   + KM K  EK       Y+   + I+N++L +RF  + IE L   LR+++  +
Sbjct: 252 FAFIESEYGKMIKKLEKHDSRHPDYLAHRDAIANKLLEVRFATRQIESLSGNLRSRVENI 311

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
            ++E++I +I +++  M R +FI+ F     NL WV+ E      ++  L R   +I E 
Sbjct: 312 RKLEREIRDICLDRVHMERDYFIQNFLPEITNLKWVEEEVAKGRVWSDALDRFRHAILEK 371

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
           Q +L N++ +  + + +L++IN+ M++ E +   AK+EM +ANLRLVISIAKKYT+RGLQ
Sbjct: 372 QTELANMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQ 431

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 432 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 491

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ LQETG EPD + +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLG
Sbjct: 492 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLG 551

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED N +AP+DAA+  S+  V K+IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 552 DFIEDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 611

Query: 607 DVTRERIRQIEAKALRKLR-PLAHDWL 632
           DVTRERIRQIEAKALRKLR P   D L
Sbjct: 612 DVTRERIRQIEAKALRKLRHPTRSDRL 638


>gi|417956969|ref|ZP_12599900.1| RNA polymerase sigma factor RpoD [Neisseria weaveri ATCC 51223]
 gi|343969401|gb|EGV37615.1| RNA polymerase sigma factor RpoD [Neisseria weaveri ATCC 51223]
          Length = 614

 Score =  625 bits (1613), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 330/612 (53%), Positives = 443/612 (72%), Gaps = 18/612 (2%)

Query: 839  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSD- 897
            +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D E ++LS+  +  
Sbjct: 1    MGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPDAEDILLSDNAAGM 60

Query: 898  --DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
              DD     EAALS+VDS+FGRT DP++MYMREMG V+LLTR+ EI IAK+IE  LK+M+
Sbjct: 61   TDDDAVAEAEAALSSVDSEFGRTTDPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMV 120

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN------- 1008
             AIS+CP +I +IL   +++  +EIK+DE+V+ +ID N    N +  G+   +       
Sbjct: 121  QAISACPGSISDILELIERVRADEIKVDEVVEAIIDSNEVLLNELGLGHLEQSGGMENSE 180

Query: 1009 --------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
                    +E+ + E+ +  +S   LE+LK + L  F  I   +DKM    +K      S
Sbjct: 181  DPEDESDPDEEDVDEADAEAISATNLEELKAKVLDHFEQIRTDYDKMVVQLKKHDSRHPS 240

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
            Y+K  + I+ ++L +RF  + IE L  +LRN++  + ++E++I +I + +  M R +FI+
Sbjct: 241  YLKHRDAIAAKLLEVRFATRQIENLSSSLRNRVENIRKLEREIRDICLERVHMERDYFIQ 300

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  +  +L+WV+NE      ++  L R   +I E Q  L +++    + + +L++IN+ 
Sbjct: 301  NFLPSITDLDWVNNEINKGRVWSNALDRFRHAIIEKQTFLSDMEKQAQISIEELKEINKN 360

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 361  MVVSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 420

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G EPD + +A
Sbjct: 421  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQENGEEPDSAKLA 480

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
              MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA+ +S+R V 
Sbjct: 481  ELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADAAMYSSLREVT 540

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R 
Sbjct: 541  KDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 600

Query: 1421 YKLKIFLEGKKN 1432
             +LK FL+ +++
Sbjct: 601  DRLKSFLDSEEH 612



 Score =  609 bits (1571), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 326/603 (54%), Positives = 433/603 (71%), Gaps = 19/603 (3%)

Query: 49  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSD- 107
           +GKERGY+T+SEIND LP+D+ D E I++I+     + I V+E   D E ++LS+  +  
Sbjct: 1   MGKERGYITYSEINDALPDDMSDAEQIDNIVSMISGLGIQVTEQAPDAEDILLSDNAAGM 60

Query: 108 --DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
             DD     EAALS+VDS+FGRT DP++MYMREMG V+LLTR+ EI IAK+IE  LK+M+
Sbjct: 61  TDDDAVAEAEAALSSVDSEFGRTTDPVRMYMREMGQVDLLTREDEIIIAKKIENALKNMV 120

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN------- 218
            AIS+CP +I +IL   +++  +EIK+DE+V+ +ID N    N +  G+   +       
Sbjct: 121 QAISACPGSISDILELIERVRADEIKVDEVVEAIIDSNEVLLNELGLGHLEQSGGMENSE 180

Query: 219 --------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
                   +E+ + E+ +  +S   LE+LK + L  F  I   +DKM    +K      S
Sbjct: 181 DPEDESDPDEEDVDEADAEAISATNLEELKAKVLDHFEQIRTDYDKMVVQLKKHDSRHPS 240

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
           Y+K  + I+ ++L +RF  + IE L  +LRN++  + ++E++I +I + +  M R +FI+
Sbjct: 241 YLKHRDAIAAKLLEVRFATRQIENLSSSLRNRVENIRKLEREIRDICLERVHMERDYFIQ 300

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  +  +L+WV+NE      ++  L R   +I E Q  L +++    + + +L++IN+ 
Sbjct: 301 NFLPSITDLDWVNNEINKGRVWSNALDRFRHAIIEKQTFLSDMEKQAQISIEELKEINKN 360

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M+  E +   AK+EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 361 MVVSEKETSAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 420

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G EPD + +A
Sbjct: 421 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQENGEEPDSAKLA 480

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
             MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA+ +S+R V 
Sbjct: 481 ELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADAAMYSSLREVT 540

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAH 629
           KD+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   
Sbjct: 541 KDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 600

Query: 630 DWL 632
           D L
Sbjct: 601 DRL 603


>gi|344200478|ref|YP_004784804.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus ferrivorans
            SS3]
 gi|343775922|gb|AEM48478.1| RNA polymerase, sigma 70 subunit, RpoD [Acidithiobacillus ferrivorans
            SS3]
          Length = 629

 Score =  624 bits (1610), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 326/615 (53%), Positives = 436/615 (70%), Gaps = 12/615 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 11   ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDG 70

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDS---DFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            ETL+     S    +EA EAA   +     D GRT DP++MYMREMGSVELLTR+GEIEI
Sbjct: 71   ETLLDGEGGSVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIEI 130

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-------SS 996
            A+RIE+GL  ++ A+S+CPTTI  +L AAD++ + E ++DE+VD  ID N        + 
Sbjct: 131  ARRIEDGLMQVLRAVSTCPTTISLLLDAADRVERGETRLDEVVDAFIDPNALDAEAVSAD 190

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
             + V+ G      E    ES   D+  ++  +L+ E+L +F+ I   +  +  ++     
Sbjct: 191  EDAVLVGGDEIEVEDDDEESEDGDVEVDKGPQLE-EALERFAVIRAAYTMLLVSYADGEM 249

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            + E+Y +    ++   L I+   + I+ + D LR    +V Q E++++E+ + +   PR 
Sbjct: 250  HGEAYQQQRRELAERFLEIKLNVRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRK 309

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F++ +P +E ++ WVD +      Y+  L      I  + ++L N++    LP+ ++++
Sbjct: 310  DFVRSYPGHESDVGWVDQQISGGFSYSARLIEFRDDIVSIMKRLANIEKRAGLPVVEIKE 369

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
             +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 370  ASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 429

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 430  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 489

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+D+A+NA++
Sbjct: 490  EELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAI 549

Query: 1357 RSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550  REVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609

Query: 1416 HPSRYYKLKIFLEGK 1430
            HPSR  +L+ F++G+
Sbjct: 610  HPSRSERLRSFVDGE 624



 Score =  607 bits (1564), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 319/600 (53%), Positives = 424/600 (70%), Gaps = 12/600 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 11  ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDG 70

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDS---DFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           ETL+     S    +EA EAA   +     D GRT DP++MYMREMGSVELLTR+GEIEI
Sbjct: 71  ETLLDGEGGSVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIEI 130

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-------SS 206
           A+RIE+GL  ++ A+S+CPTTI  +L AAD++ + E ++DE+VD  ID N        + 
Sbjct: 131 ARRIEDGLMQVLRAVSTCPTTISLLLDAADRVERGETRLDEVVDAFIDPNALDAEAVSAD 190

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
            + V+ G      E    ES   D+  ++  +L+ E+L +F+ I   +  +  ++     
Sbjct: 191 EDAVLVGGDEIEVEDDDEESEDGDVEVDKGPQLE-EALERFAVIRAAYTMLLVSYADGEM 249

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           + E+Y +    ++   L I+   + I+ + D LR    +V Q E++++E+ + +   PR 
Sbjct: 250 HGEAYQQQRRELAERFLEIKLNVRQIDVMTDALRGLTEEVRQCERELMELCIERARFPRK 309

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F++ +P +E ++ WVD +      Y+  L      I  + ++L N++    LP+ ++++
Sbjct: 310 DFVRSYPGHESDVGWVDQQISGGFSYSARLIEFRDDIVSIMKRLANIEKRAGLPVVEIKE 369

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
            +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 370 ASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 429

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 430 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 489

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+D+A+NA++
Sbjct: 490 EELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTAPADSAVNAAI 549

Query: 567 RSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 REVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|198284073|ref|YP_002220394.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus ferrooxidans
            ATCC 53993]
 gi|198248594|gb|ACH84187.1| RNA polymerase, sigma 70 subunit, RpoD [Acidithiobacillus
            ferrooxidans ATCC 53993]
          Length = 631

 Score =  624 bits (1609), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 326/625 (52%), Positives = 441/625 (70%), Gaps = 30/625 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 11   ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 70

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 71   DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 130

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 131  IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 188

Query: 1003 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 1046
               +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 189  ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 241

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 242  LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 301

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 302  CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 361

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              LP+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 362  AGLPIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 421

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 422  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 481

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 482  LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 541

Query: 1347 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 542  PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 601

Query: 1406 IEAKALRKLRHPSRYYKLKIFLEGK 1430
            IEAKALRKLRHPSR  +L+ F++G+
Sbjct: 602  IEAKALRKLRHPSRSERLRSFVDGE 626



 Score =  606 bits (1563), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 319/610 (52%), Positives = 429/610 (70%), Gaps = 30/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 11  ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 70

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 71  DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 130

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 131 IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 188

Query: 213 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 256
              +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 189 ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 241

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 242 LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 301

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 302 CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 361

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             LP+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 362 AGLPIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 421

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 422 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 481

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 482 LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 541

Query: 557 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 542 PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 601

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 602 IEAKALRKLR 611


>gi|255019635|ref|ZP_05291715.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
            51756]
 gi|254970938|gb|EET28420.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus ATCC
            51756]
          Length = 625

 Score =  624 bits (1609), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 326/622 (52%), Positives = 442/622 (71%), Gaps = 23/622 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R + K LI  GKE+GYLT+ EIND LPED+ D E +E++I     M I V E   D 
Sbjct: 4    ESQRSELKRLIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDD 63

Query: 887  ETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            ETL++ N    I +  + EEA E AL+ V++D GRT DP++MYMREMG+VELLTR+GEIE
Sbjct: 64   ETLLMDNEGNPIVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGTVELLTREGEIE 123

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------- 993
            IA+RIE+GL  ++ A+S+CPTTI  +L AA K+ + E+++DE+VD  ID N         
Sbjct: 124  IARRIEDGLLQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVDAFIDPNAINEAAAED 183

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 ++          + +E+     S AD    QLE    E+L +F+ I   ++ +  
Sbjct: 184  EDLGLAAEADEADDGDEDEDEEDGAGLSVAD-KGPQLE----EALERFAAIRAGYEHLLA 238

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              +     S  Y +    +++  + ++   + I+ + D LRN   +V   E++++ + ++
Sbjct: 239  LHKAGKVRSPEYQEQRQLLADRFMEMKLNVRQIDLMADALRNLTEEVRLAERELMALCID 298

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            + G PR  F++ +P +E ++ WVD +      Y+ ++      I  +  +L +++    L
Sbjct: 299  RAGFPRKEFVRSYPGHESDIAWVDAQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGL 358

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            P+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359  PIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 419  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 478

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+D
Sbjct: 479  MGREPTPEELAARMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTD 538

Query: 1350 AALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            AA+NA++R VV+++L++ LTPRE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 539  AAVNAAIREVVEELLDTGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEA 598

Query: 1409 KALRKLRHPSRYYKLKIFLEGK 1430
            KALRKLRHPSR  +L+ F++G+
Sbjct: 599  KALRKLRHPSRSERLRSFVDGE 620



 Score =  606 bits (1563), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 319/607 (52%), Positives = 430/607 (70%), Gaps = 23/607 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R + K LI  GKE+GYLT+ EIND LPED+ D E +E++I     M I V E   D 
Sbjct: 4   ESQRSELKRLIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDD 63

Query: 97  ETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           ETL++ N    I +  + EEA E AL+ V++D GRT DP++MYMREMG+VELLTR+GEIE
Sbjct: 64  ETLLMDNEGNPIVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGTVELLTREGEIE 123

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------- 203
           IA+RIE+GL  ++ A+S+CPTTI  +L AA K+ + E+++DE+VD  ID N         
Sbjct: 124 IARRIEDGLLQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVDAFIDPNAINEAAAED 183

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                ++          + +E+     S AD    QLE    E+L +F+ I   ++ +  
Sbjct: 184 EDLGLAAEADEADDGDEDEDEEDGAGLSVAD-KGPQLE----EALERFAAIRAGYEHLLA 238

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             +     S  Y +    +++  + ++   + I+ + D LRN   +V   E++++ + ++
Sbjct: 239 LHKAGKVRSPEYQEQRQLLADRFMEMKLNVRQIDLMADALRNLTEEVRLAERELMALCID 298

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           + G PR  F++ +P +E ++ WVD +      Y+ ++      I  +  +L +++    L
Sbjct: 299 RAGFPRKEFVRSYPGHESDIAWVDAQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGL 358

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
           P+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359 PIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 419 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 478

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+D
Sbjct: 479 MGREPTPEELAARMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTD 538

Query: 560 AALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           AA+NA++R VV+++L++ LTPRE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 539 AAVNAAIREVVEELLDTGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEA 598

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 599 KALRKLR 605


>gi|218665974|ref|YP_002426728.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans ATCC
            23270]
 gi|218518187|gb|ACK78773.1| RNA polymerase sigma factor RpoD [Acidithiobacillus ferrooxidans ATCC
            23270]
          Length = 624

 Score =  623 bits (1607), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 326/625 (52%), Positives = 441/625 (70%), Gaps = 30/625 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 4    ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 63

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 64   DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 123

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 124  IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 181

Query: 1003 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 1046
               +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 182  ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 234

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 235  LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 294

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 295  CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 354

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              LP+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 355  AGLPIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 414

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 415  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 474

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 475  LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 534

Query: 1347 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 535  PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 594

Query: 1406 IEAKALRKLRHPSRYYKLKIFLEGK 1430
            IEAKALRKLRHPSR  +L+ F++G+
Sbjct: 595  IEAKALRKLRHPSRSERLRSFVDGE 619



 Score =  605 bits (1561), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 319/610 (52%), Positives = 429/610 (70%), Gaps = 30/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 4   ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 63

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 64  DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 123

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 124 IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 181

Query: 213 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 256
              +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 182 ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 234

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 235 LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 294

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 295 CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 354

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             LP+ ++++ +R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 355 AGLPIAEIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 414

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 415 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 474

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 475 LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 534

Query: 557 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 535 PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 594

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 595 IEAKALRKLR 604


>gi|415973851|ref|ZP_11558723.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus sp. GGI-221]
 gi|339833812|gb|EGQ61624.1| RNA polymerase sigma-70 subunit RpoD [Acidithiobacillus sp. GGI-221]
          Length = 624

 Score =  621 bits (1601), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 325/625 (52%), Positives = 440/625 (70%), Gaps = 30/625 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 4    ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 63

Query: 887  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 64   DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 123

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 124  IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 181

Query: 1003 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 1046
               +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 182  ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 234

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 235  LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 294

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 295  CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 354

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              LP+ ++++ +  M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 355  AGLPIAEIKEASHLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 414

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 415  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 474

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 475  LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 534

Query: 1347 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 535  PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 594

Query: 1406 IEAKALRKLRHPSRYYKLKIFLEGK 1430
            IEAKALRKLRHPSR  +L+ F++G+
Sbjct: 595  IEAKALRKLRHPSRSERLRSFVDGE 619



 Score =  603 bits (1555), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 318/610 (52%), Positives = 428/610 (70%), Gaps = 30/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R + K LI  GKE+GYLT+ EIND LPE++ D E +E++I     M I V E   D 
Sbjct: 4   ESQRSELKRLIARGKEQGYLTYREINDHLPEEVFDPEQMENVISMINDMGIEVFEEAPDD 63

Query: 97  ETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +TL++      + +  + EEA E AL+ V++D GRT DP++MYMREMGSVELLTR+GEIE
Sbjct: 64  DTLLMDGEGGTVVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGSVELLTREGEIE 123

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IA+RIE+GL  ++ A+S+CPTTI  +L AA ++ + E ++DE+VD  ID +      V  
Sbjct: 124 IARRIEDGLMQVLRAVSTCPTTISLLLDAAARVERGETRLDEVVDAFIDLSALDAETV-- 181

Query: 213 GNKNNNEEKILIESSSADLSTE----------------QLEKLKYESLIKFSNISFHFDK 256
              +  EE +L+E    D+  +                QLE    ++L +F+ I   +  
Sbjct: 182 ---SEAEESVLVEGDDLDVDEDEEESEDGDIEVVDKGPQLE----DALERFAVIRAAYTA 234

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           +  +  +   + ESY +    ++   L I+   + I+ + D LR    +V Q E++++E+
Sbjct: 235 LLASHAEGEMHGESYQRQRRELAERFLEIKLNGRQIDVMTDALRGLTEEVRQCERELMEL 294

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            + +   PR  F++ +P +E ++ W+D +    H Y+  L      I  + ++L N++  
Sbjct: 295 CIERARFPRKEFVRSYPGHEGDIGWIDQQIAAGHAYSTRLVEFRDDIVAIMKRLANIEKR 354

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             LP+ ++++ +  M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 355 AGLPIAEIKEASHLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 414

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 415 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 474

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ A
Sbjct: 475 LQEMGREPSPEELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVTA 534

Query: 557 PSDAALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           P+D+A+NA++R VV+++L N LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 535 PADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQ 594

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 595 IEAKALRKLR 604


>gi|289207448|ref|YP_003459514.1| RNA polymerase sigma-70 subunit RpoD [Thioalkalivibrio sp. K90mix]
 gi|288943079|gb|ADC70778.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp. K90mix]
          Length = 629

 Score =  620 bits (1600), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 440/629 (69%), Gaps = 28/629 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GKE+GYLT++E+ND LP+ IID + +E II     M I+V E   D 
Sbjct: 4    EEQQSQLKELIAKGKEQGYLTYTEVNDHLPDSIIDSDQVEDIIAMINDMGIAVHEQAPDA 63

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++L+LS+  +++D+D E+A  AAL++ DSDFGRT DP++MYMREMG+VELLTR+GEI IA
Sbjct: 64   DSLLLSDGSVSADEDAEDAV-AALASADSDFGRTTDPVRMYMREMGTVELLTREGEIRIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-KNFSSNNRVIKG 1003
            KRIEEGL  ++ A++  P  I  ++   D+I +N  ++ ++V   ID KN      V +G
Sbjct: 123  KRIEEGLMQVLFALAHHPGAIEHLIREYDQIVENNGRLTDLVVSFIDPKNPLDGEAVARG 182

Query: 1004 --NKNNNEEKILIESSSADLSTEQLEKLKY--------------------ESLIKFSNIS 1041
              +  + ++    + ++A  ++ +L+ +                      E+  +F+ + 
Sbjct: 183  LVSPEDAQKAEEAQKAAAAEASPELDAIVEEVEDAEEEDAEPVDTGPDPEEARERFNKLR 242

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
                K  KAFEK   + ++Y  A    +   +  +   + +++L   L   I+++   E+
Sbjct: 243  KLHAKAHKAFEK--GDRKAYATAREATAKYFMEFKLVPRMVDQLTTKLHGTIDRIRSHER 300

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
            +I+E+ VN+  MPR  FI  FP+NE NL+W+    K +  Y   L  +   I  LQ+KL 
Sbjct: 301  RIMELAVNQAQMPRKSFIDSFPKNETNLDWIKQACKAKGKYTTALAEHEDEIVRLQKKLA 360

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++ +  L ++++++INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 361  EIEHEASLNISEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 420

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 421  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 480

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            +SRQ+LQE G E  P  +A +MEMPE+KIRK++KI+KEP+SME+P+GDDEDSHLGDFIED
Sbjct: 481  VSRQMLQEMGREATPEELAERMEMPEDKIRKVLKISKEPISMETPIGDDEDSHLGDFIED 540

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
            E + +PSD+A   S+    ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 541  EKVASPSDSAARESLSEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 600

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            RIRQIEAKALRKLRHP+R   L+ + + +
Sbjct: 601  RIRQIEAKALRKLRHPTRAELLRTYTDAE 629



 Score =  610 bits (1572), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 315/614 (51%), Positives = 431/614 (70%), Gaps = 28/614 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GKE+GYLT++E+ND LP+ IID + +E II     M I+V E   D 
Sbjct: 4   EEQQSQLKELIAKGKEQGYLTYTEVNDHLPDSIIDSDQVEDIIAMINDMGIAVHEQAPDA 63

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++L+LS+  +++D+D E+A  AAL++ DSDFGRT DP++MYMREMG+VELLTR+GEI IA
Sbjct: 64  DSLLLSDGSVSADEDAEDAV-AALASADSDFGRTTDPVRMYMREMGTVELLTREGEIRIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-KNFSSNNRVIKG 213
           KRIEEGL  ++ A++  P  I  ++   D+I +N  ++ ++V   ID KN      V +G
Sbjct: 123 KRIEEGLMQVLFALAHHPGAIEHLIREYDQIVENNGRLTDLVVSFIDPKNPLDGEAVARG 182

Query: 214 --NKNNNEEKILIESSSADLSTEQLEKLKY--------------------ESLIKFSNIS 251
             +  + ++    + ++A  ++ +L+ +                      E+  +F+ + 
Sbjct: 183 LVSPEDAQKAEEAQKAAAAEASPELDAIVEEVEDAEEEDAEPVDTGPDPEEARERFNKLR 242

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
               K  KAFEK   + ++Y  A    +   +  +   + +++L   L   I+++   E+
Sbjct: 243 KLHAKAHKAFEK--GDRKAYATAREATAKYFMEFKLVPRMVDQLTTKLHGTIDRIRSHER 300

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 371
           +I+E+ VN+  MPR  FI  FP+NE NL+W+    K +  Y   L  +   I  LQ+KL 
Sbjct: 301 RIMELAVNQAQMPRKSFIDSFPKNETNLDWIKQACKAKGKYTTALAEHEDEIVRLQKKLA 360

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            ++ +  L ++++++INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 361 EIEHEASLNISEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 420

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 421 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 480

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           +SRQ+LQE G E  P  +A +MEMPE+KIRK++KI+KEP+SME+P+GDDEDSHLGDFIED
Sbjct: 481 VSRQMLQEMGREATPEELAERMEMPEDKIRKVLKISKEPISMETPIGDDEDSHLGDFIED 540

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
           E + +PSD+A   S+    ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 541 EKVASPSDSAARESLSEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 600

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 601 RIRQIEAKALRKLR 614


>gi|83746506|ref|ZP_00943557.1| RpoD [Ralstonia solanacearum UW551]
 gi|83726837|gb|EAP73964.1| RpoD [Ralstonia solanacearum UW551]
          Length = 391

 Score =  620 bits (1598), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 291/387 (75%), Positives = 341/387 (88%)

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
              +KMR AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V ++E+ 
Sbjct: 4    RLEKMRSAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERA 63

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQKLI+
Sbjct: 64   ILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQKLID 123

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 124  LQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQ 183

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 184  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRI 243

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED 
Sbjct: 244  SRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDT 303

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
            N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRER
Sbjct: 304  NTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRER 363

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            IRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 364  IRQIEAKALRKLRHPSRSDKLKSFLEG 390



 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 280/373 (75%), Positives = 330/373 (88%)

Query: 253 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
             +KMR AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V ++E+ 
Sbjct: 4   RLEKMRSAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRKLERA 63

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
           IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQKLI+
Sbjct: 64  ILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQKLID 123

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
           LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 124 LQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQ 183

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 184 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRI 243

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SRQILQETG+EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED 
Sbjct: 244 SRQILQETGNEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDT 303

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
           N LAP++AAL+ SMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEVGKQFDVTRER
Sbjct: 304 NTLAPAEAALHGSMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRER 363

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 364 IRQIEAKALRKLR 376


>gi|340783004|ref|YP_004749611.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus SM-1]
 gi|340557155|gb|AEK58909.1| RNA polymerase sigma factor RpoD [Acidithiobacillus caldus SM-1]
          Length = 613

 Score =  619 bits (1597), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 322/613 (52%), Positives = 437/613 (71%), Gaps = 23/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 893
            +I  GKE+GYLT+ EIND LPED+ D E +E++I     M I V E   D ETL++ N  
Sbjct: 1    MIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDDETLLMDNEG 60

Query: 894  --ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
              I +  + EEA E AL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIA+RIE+GL
Sbjct: 61   NPIVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGTVELLTREGEIEIARRIEDGL 120

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------------FSSNN 998
              ++ A+S+CPTTI  +L AA K+ + E+++DE+VD  ID N              ++  
Sbjct: 121  LQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVDAFIDPNAINEAAAEDEDLGLAAEA 180

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
                    + +E+     S AD    QLE    E+L +F+ I   ++ +    +     S
Sbjct: 181  DEADDGDEDEDEEDGAGLSVAD-KGPQLE----EALERFAAIRAGYEHLLALHKAGKVRS 235

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
              Y +    +++  + ++   + I+ + D LRN   +V   E++++ + +++ G PR  F
Sbjct: 236  PEYQEQRQLLADRFMEMKLNVRQIDLMADALRNLTEEVRLAERELMALCIDRAGFPRKEF 295

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            ++ +P +E ++ WVD +      Y+ ++      I  +  +L +++    LP+ ++++ +
Sbjct: 296  VRSYPGHESDIAWVDAQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGLPIAEIKEAS 355

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 356  RLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 415

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 416  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 475

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+DAA+NA++R 
Sbjct: 476  LAARMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTDAAVNAAIRE 535

Query: 1359 VVKDILNS-LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            VV+++L++ LTPRE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 536  VVEELLDTGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 595

Query: 1418 SRYYKLKIFLEGK 1430
            SR  +L+ F++G+
Sbjct: 596  SRSERLRSFVDGE 608



 Score =  602 bits (1551), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/598 (52%), Positives = 425/598 (71%), Gaps = 23/598 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 103
           +I  GKE+GYLT+ EIND LPED+ D E +E++I     M I V E   D ETL++ N  
Sbjct: 1   MIARGKEQGYLTYREINDLLPEDVFDPEQMENVITMINDMGIEVFEEAPDDETLLMDNEG 60

Query: 104 --ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
             I +  + EEA E AL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIA+RIE+GL
Sbjct: 61  NPIVAAQEAEEAAEEALAVVEADIGRTSDPVRMYMREMGTVELLTREGEIEIARRIEDGL 120

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------------FSSNN 208
             ++ A+S+CPTTI  +L AA K+ + E+++DE+VD  ID N              ++  
Sbjct: 121 LQVLRAVSTCPTTIALLLEAAQKVEQGELRLDEVVDAFIDPNAINEAAAEDEDLGLAAEA 180

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
                   + +E+     S AD    QLE    E+L +F+ I   ++ +    +     S
Sbjct: 181 DEADDGDEDEDEEDGAGLSVAD-KGPQLE----EALERFAAIRAGYEHLLALHKAGKVRS 235

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
             Y +    +++  + ++   + I+ + D LRN   +V   E++++ + +++ G PR  F
Sbjct: 236 PEYQEQRQLLADRFMEMKLNVRQIDLMADALRNLTEEVRLAERELMALCIDRAGFPRKEF 295

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           ++ +P +E ++ WVD +      Y+ ++      I  +  +L +++    LP+ ++++ +
Sbjct: 296 VRSYPGHESDIAWVDAQIAAGRPYSPMMLVLRDEIVAVMTQLADIEERAGLPIAEIKEAS 355

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 356 RLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 415

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 416 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 475

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ AP+DAA+NA++R 
Sbjct: 476 LAARMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDRNVAAPTDAAVNAAIRE 535

Query: 569 VVKDILNS-LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VV+++L++ LTPRE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 536 VVEELLDTGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 593


>gi|390576239|ref|ZP_10256311.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia terrae BS001]
 gi|389931775|gb|EIM93831.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia terrae BS001]
          Length = 665

 Score =  619 bits (1596), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 291/620 (46%), Positives = 427/620 (68%), Gaps = 16/620 (2%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            ++ E+ + +   LI+LGKERG LT ++IND LP+     + IESI+ TF  M ++V E  
Sbjct: 44   QQAEHTQNQMLALIQLGKERGLLTHADINDHLPDGFARTDAIESIVHTFSDMGVAVYEKA 103

Query: 884  LDTETLM---LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
             D +TL+      +  D   +E +E ALS +DS+FGRT DP+ MYMREMG++ELLTR GE
Sbjct: 104  SDAQTLLNDTAPTVALDAQADEESEVALSAIDSEFGRTTDPVSMYMREMGAIELLTRAGE 163

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--- 997
            IEIAKRIE+ L++MI AI++CP T+  +L +A++I+  E++IDE+VDGL +     +   
Sbjct: 164  IEIAKRIEDSLREMIQAIAACPATVSALLASAEQIAAGELRIDELVDGLYEDTMQDDLPP 223

Query: 998  ----------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
                       + I  + +++E+  L  + +   +  Q ++L    L  F+ +   F+++
Sbjct: 224  SDSDTAPDIETKAIDSDADSDEDGRLEAAGATPANEAQPKQLTSACLAIFTRVRELFEQL 283

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
             + +  +   S  + +    I  E+  IRFTA++I++L   ++ Q+ QV  IE++IL++ 
Sbjct: 284  PRPYSTKDIASAEFARVRGEIQRELASIRFTARTIDRLSTDVQQQVAQVRAIERRILQVA 343

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V +CGMPR  F++ FP +E +L W          +   L  ++P ++  QQKLIN++  +
Sbjct: 344  VVRCGMPRETFVESFPAHETDLGWTAWTAATSSAFGAALEGSLPEVQAEQQKLINIEAKL 403

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             LPL  L+ +NR+M   E K  +AKREM EANLRLVISIA+KY +RG+Q LDLIQEGNIG
Sbjct: 404  ALPLQQLKQVNRQMTVAEAKMLQAKREMIEANLRLVISIARKYVNRGVQLLDLIQEGNIG 463

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRG+KFSTYATWW++QA+TR++ADQ RTIR+PVH   T+ K++RI+ +IL
Sbjct: 464  LMKAVDKFEYRRGWKFSTYATWWVKQAVTRALADQGRTIRVPVHTSATVKKLNRIAHEIL 523

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            Q+TG E    +I+++M MPE+K+  IMKI KEP+S+E+PVG+D D+ LG+ IED +  +P
Sbjct: 524  QQTGQEAHLKMISVRMGMPEKKVLGIMKIVKEPLSLETPVGEDADATLGEIIEDSSATSP 583

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            +DAA +A MR+ V++ L+SL+PRE+KVLRMRFGI+ +S HTLEE+GK+FDV+RERIRQIE
Sbjct: 584  ADAAEHADMRAAVQEALDSLSPREAKVLRMRFGIDTTSAHTLEEIGKKFDVSRERIRQIE 643

Query: 1408 AKALRKLRHPSRYYKLKIFL 1427
            ++A+R L HPSR  KL+  L
Sbjct: 644  SEAMRTLTHPSRSNKLRSLL 663



 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 284/607 (46%), Positives = 419/607 (69%), Gaps = 16/607 (2%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           ++ E+ + +   LI+LGKERG LT ++IND LP+     + IESI+ TF  M ++V E  
Sbjct: 44  QQAEHTQNQMLALIQLGKERGLLTHADINDHLPDGFARTDAIESIVHTFSDMGVAVYEKA 103

Query: 94  LDTETLM---LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
            D +TL+      +  D   +E +E ALS +DS+FGRT DP+ MYMREMG++ELLTR GE
Sbjct: 104 SDAQTLLNDTAPTVALDAQADEESEVALSAIDSEFGRTTDPVSMYMREMGAIELLTRAGE 163

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--- 207
           IEIAKRIE+ L++MI AI++CP T+  +L +A++I+  E++IDE+VDGL +     +   
Sbjct: 164 IEIAKRIEDSLREMIQAIAACPATVSALLASAEQIAAGELRIDELVDGLYEDTMQDDLPP 223

Query: 208 ----------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
                      + I  + +++E+  L  + +   +  Q ++L    L  F+ +   F+++
Sbjct: 224 SDSDTAPDIETKAIDSDADSDEDGRLEAAGATPANEAQPKQLTSACLAIFTRVRELFEQL 283

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
            + +  +   S  + +    I  E+  IRFTA++I++L   ++ Q+ QV  IE++IL++ 
Sbjct: 284 PRPYSTKDIASAEFARVRGEIQRELASIRFTARTIDRLSTDVQQQVAQVRAIERRILQVA 343

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V +CGMPR  F++ FP +E +L W          +   L  ++P ++  QQKLIN++  +
Sbjct: 344 VVRCGMPRETFVESFPAHETDLGWTAWTAATSSAFGAALEGSLPEVQAEQQKLINIEAKL 403

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            LPL  L+ +NR+M   E K  +AKREM EANLRLVISIA+KY +RG+Q LDLIQEGNIG
Sbjct: 404 ALPLQQLKQVNRQMTVAEAKMLQAKREMIEANLRLVISIARKYVNRGVQLLDLIQEGNIG 463

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRG+KFSTYATWW++QA+TR++ADQ RTIR+PVH   T+ K++RI+ +IL
Sbjct: 464 LMKAVDKFEYRRGWKFSTYATWWVKQAVTRALADQGRTIRVPVHTSATVKKLNRIAHEIL 523

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           Q+TG E    +I+++M MPE+K+  IMKI KEP+S+E+PVG+D D+ LG+ IED +  +P
Sbjct: 524 QQTGQEAHLKMISVRMGMPEKKVLGIMKIVKEPLSLETPVGEDADATLGEIIEDSSATSP 583

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           +DAA +A MR+ V++ L+SL+PRE+KVLRMRFGI+ +S HTLEE+GK+FDV+RERIRQIE
Sbjct: 584 ADAAEHADMRAAVQEALDSLSPREAKVLRMRFGIDTTSAHTLEEIGKKFDVSRERIRQIE 643

Query: 618 AKALRKL 624
           ++A+R L
Sbjct: 644 SEAMRTL 650


>gi|350552445|ref|ZP_08921646.1| RNA polymerase, sigma 70 subunit, RpoD [Thiorhodospira sibirica ATCC
            700588]
 gi|349794184|gb|EGZ48004.1| RNA polymerase, sigma 70 subunit, RpoD [Thiorhodospira sibirica ATCC
            700588]
          Length = 673

 Score =  618 bits (1594), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 324/631 (51%), Positives = 441/631 (69%), Gaps = 38/631 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E   D 
Sbjct: 50   EEQQSRLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIFMINNMGIAVHEQAPDA 109

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            +TL+LS+  +T+DDD  E   AAL++VD +FGRT DP++MYMREMG+VELLTRDGEI+IA
Sbjct: 110  DTLLLSDTGVTADDDAAEEAAAALASVDGEFGRTTDPVRMYMREMGTVELLTRDGEIQIA 169

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------KNFSSNN 998
            KRIEEGL  ++ A++  P +I  +L   +K+   EIK+ +++ G +D       N S+ +
Sbjct: 170  KRIEEGLAQVLFALAHYPQSIASLLAEYEKVQSEEIKLSDVLVGFMDITTGDVVNSSAPD 229

Query: 999  RVIKGNKNN----------------NEEKILIESSSADLSTEQLEKLKYESLIKFSNISF 1042
              +  ++NN                +EE   + S+  DL     +  + +          
Sbjct: 230  SELLDDENNVTAMEASDDDVDSVSNDEEDEEVASAEDDLVDAGPDPEEAQE--------- 280

Query: 1043 HFDKMRKAFEK-----EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
             F K+R+ +E+     E    E Y +A   +++  + ++   + +++L   L   + ++ 
Sbjct: 281  RFSKLREMYERAVGFAEKKQKEKYRQAREELAHYFMEMKLVPRLVDQLTIDLHGVVERIR 340

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
              E+ +++  +N+C MPR  FI  FPENE NL W+D   K +  Y   L +N   I  +Q
Sbjct: 341  SHERAVMDTCINRCKMPRKDFIHSFPENETNLKWLDGLVKEKTPYAAALQQNKDEILRIQ 400

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            ++L+ ++ +  L +++++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 401  KQLVAIEEETGLSISEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 460

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 461  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 520

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G E  P  ++ +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 521  KLNRISRQMLQEMGREATPEELSRRMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGD 580

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED N+++P ++A   S+    +D+L+SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 581  FIEDSNVMSPIESATRESLSETTRDVLSSLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 640

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 641  VTRERIRQIEAKALRKLRHPSRSEMLRSFLD 671



 Score =  604 bits (1557), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 317/618 (51%), Positives = 432/618 (69%), Gaps = 38/618 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E   D 
Sbjct: 50  EEQQSRLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIFMINNMGIAVHEQAPDA 109

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           +TL+LS+  +T+DDD  E   AAL++VD +FGRT DP++MYMREMG+VELLTRDGEI+IA
Sbjct: 110 DTLLLSDTGVTADDDAAEEAAAALASVDGEFGRTTDPVRMYMREMGTVELLTRDGEIQIA 169

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------KNFSSNN 208
           KRIEEGL  ++ A++  P +I  +L   +K+   EIK+ +++ G +D       N S+ +
Sbjct: 170 KRIEEGLAQVLFALAHYPQSIASLLAEYEKVQSEEIKLSDVLVGFMDITTGDVVNSSAPD 229

Query: 209 RVIKGNKNN----------------NEEKILIESSSADLSTEQLEKLKYESLIKFSNISF 252
             +  ++NN                +EE   + S+  DL     +  + +          
Sbjct: 230 SELLDDENNVTAMEASDDDVDSVSNDEEDEEVASAEDDLVDAGPDPEEAQE--------- 280

Query: 253 HFDKMRKAFEK-----EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
            F K+R+ +E+     E    E Y +A   +++  + ++   + +++L   L   + ++ 
Sbjct: 281 RFSKLREMYERAVGFAEKKQKEKYRQAREELAHYFMEMKLVPRLVDQLTIDLHGVVERIR 340

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
             E+ +++  +N+C MPR  FI  FPENE NL W+D   K +  Y   L +N   I  +Q
Sbjct: 341 SHERAVMDTCINRCKMPRKDFIHSFPENETNLKWLDGLVKEKTPYAAALQQNKDEILRIQ 400

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           ++L+ ++ +  L +++++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 401 KQLVAIEEETGLSISEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 460

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 461 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 520

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G E  P  ++ +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 521 KLNRISRQMLQEMGREATPEELSRRMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGD 580

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED N+++P ++A   S+    +D+L+SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 581 FIEDSNVMSPIESATRESLSETTRDVLSSLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 640

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 641 VTRERIRQIEAKALRKLR 658


>gi|358447902|ref|ZP_09158412.1| RpoD family RNA polymerase sigma factor [Marinobacter manganoxydans
            MnI7-9]
 gi|385330056|ref|YP_005884007.1| RNA polymerase sigma-70 subunit RpoD [Marinobacter adhaerens HP15]
 gi|311693206|gb|ADP96079.1| RNA polymerase, sigma 70 subunit, RpoD [Marinobacter adhaerens HP15]
 gi|357227903|gb|EHJ06358.1| RpoD family RNA polymerase sigma factor [Marinobacter manganoxydans
            MnI7-9]
          Length = 615

 Score =  616 bits (1589), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 321/609 (52%), Positives = 432/609 (70%), Gaps = 8/609 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 7    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 66

Query: 890  MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67   LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 1003
            EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +    F   +   + 
Sbjct: 127  EEGIRDVMAAVAHFPGTAGTVIQAYDRILENEGRISDIVTGFLDPDDAEPFMGEDTTPES 186

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            + +++ +    + SS + +    +    E+ ++F  ++   +   KA  K G + +   +
Sbjct: 187  SDDSDSDSDDDDDSSEEETDNGPDP--EETRLRFELLNEKLEAANKALAKHGRSDKKTQE 244

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A N +       +   K+ ++L + +R+  + V + E+ I++I V +C MPR  FIK FP
Sbjct: 245  ALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRECKMPRKDFIKSFP 304

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+W D   K +  Y   L   I  +  LQ+++ N+QT++ L + D+++INR++  
Sbjct: 305  GNETNLDWADKIAKSKKPYAAPLAERIDEVVRLQKRIQNVQTEVDLDVADIKEINRRVSI 364

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 365  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 424

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 425  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 484

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 485  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 544

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 545  LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 604

Query: 1424 KIFLEGKKN 1432
            + F++ + N
Sbjct: 605  RGFIDDQGN 613



 Score =  601 bits (1550), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 317/600 (52%), Positives = 424/600 (70%), Gaps = 9/600 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 7   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 66

Query: 100 MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67  LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 213
           EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +    F   +   + 
Sbjct: 127 EEGIRDVMAAVAHFPGTAGTVIQAYDRILENEGRISDIVTGFLDPDDAEPFMGEDTTPES 186

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           + +++ +    + SS + +    +    E+ ++F  ++   +   KA  K G + +   +
Sbjct: 187 SDDSDSDSDDDDDSSEEETDNGPDP--EETRLRFELLNEKLEAANKALAKHGRSDKKTQE 244

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A N +       +   K+ ++L + +R+  + V + E+ I++I V +C MPR  FIK FP
Sbjct: 245 ALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRECKMPRKDFIKSFP 304

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+W D   K +  Y   L   I  +  LQ+++ N+QT++ L + D+++INR++  
Sbjct: 305 GNETNLDWADKIAKSKKPYAAPLAERIDEVVRLQKRIQNVQTEVDLDVADIKEINRRVSI 364

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 365 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 424

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 425 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 484

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 485 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 544

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 545 LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 604


>gi|207743818|ref|YP_002260210.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595218|emb|CAQ62145.1| rna polymerase sigma d (sigma-70) factor (partial sequence c
           terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 684

 Score =  613 bits (1581), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 305/517 (58%), Positives = 391/517 (75%), Gaps = 15/517 (2%)

Query: 7   KTKIKNKKTKETLLKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLP 66
           K K +++K KE  L   F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP
Sbjct: 168 KQKARDRKAKEKALLKEFAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLP 227

Query: 67  EDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVD 122
           +D++D E +++++ T   + I+V E   D ETL+L++    +T++++ EE  EAALSTVD
Sbjct: 228 DDMVDAESMDTLVATLNDIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVD 287

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+FGRT DP++MYMREMG+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   
Sbjct: 288 SEFGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMG 347

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADL 231
           ++++ +E KIDE +DGLID N  +  +                 +  E++    +  A  
Sbjct: 348 ERVANDEAKIDEYIDGLIDLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAA 407

Query: 232 STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKS 291
           S  QLE+LK  +L KFS I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA++
Sbjct: 408 SARQLEELKQAALEKFSIIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARN 467

Query: 292 IEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD 351
           +E+LCDTLR Q+++V ++E+ IL IVV+KCGM R  F+  FP NE NL W++        
Sbjct: 468 VERLCDTLRGQVDEVRKLERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKP 527

Query: 352 YNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLR 411
           Y+ I+ RNIP++ ELQQKLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLR
Sbjct: 528 YSAIVERNIPAVHELQQKLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLR 587

Query: 412 LVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471
           LVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD
Sbjct: 588 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 647

Query: 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           QARTIRIPVHMIETINK++RISRQILQETG+EPDP+ 
Sbjct: 648 QARTIRIPVHMIETINKMNRISRQILQETGNEPDPAT 684



 Score =  605 bits (1560), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 299/500 (59%), Positives = 382/500 (76%), Gaps = 15/500 (3%)

Query: 814  FSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFR 873
            F+   +  S EE+E  R+K K LIKLGK RGYLT++EIND LP+D++D E +++++ T  
Sbjct: 185  FAATQQGGSEEELEARRQKLKALIKLGKSRGYLTYAEINDHLPDDMVDAESMDTLVATLN 244

Query: 874  YMDISVSEHVLDTETLMLSN----ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREM 929
             + I+V E   D ETL+L++    +T++++ EE  EAALSTVDS+FGRT DP++MYMREM
Sbjct: 245  DIGIAVYEQAPDAETLLLNDNAPSVTTEEEAEEEAEAALSTVDSEFGRTTDPVRMYMREM 304

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELLTR+GEIEIAKRIE GLKDM+ AIS+CP TI EIL   ++++ +E KIDE +DGL
Sbjct: 305  GTVELLTREGEIEIAKRIEAGLKDMVMAISACPVTISEILAMGERVANDEAKIDEYIDGL 364

Query: 990  IDKNFSSNNR-----------VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFS 1038
            ID N  +  +                 +  E++    +  A  S  QLE+LK  +L KFS
Sbjct: 365  IDLNAEAEAQSADEDEDFEDEEADEGDDEEEDEDDDGAGGAAASARQLEELKQAALEKFS 424

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             I   F+KMR+AFEKEGY S+SY+KA   I NE++ IRFTA+++E+LCDTLR Q+++V +
Sbjct: 425  IIGDQFEKMRRAFEKEGYKSKSYLKAQEAIQNELMTIRFTARNVERLCDTLRGQVDEVRK 484

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E+ IL IVV+KCGM R  F+  FP NE NL W++        Y+ I+ RNIP++ ELQQ
Sbjct: 485  LERAILNIVVDKCGMSRGDFVSRFPGNETNLGWINTVVADGKPYSAIVERNIPAVHELQQ 544

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI+LQ+ +VLPL +L+D+N+KM  GE +AR+AKREMTEANLRLVISIAKKYT+RGLQFL
Sbjct: 545  KLIDLQSRVVLPLAELKDVNKKMSEGERRAREAKREMTEANLRLVISIAKKYTNRGLQFL 604

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 605  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 664

Query: 1279 ISRISRQILQETGSEPDPSV 1298
            ++RISRQILQETG+EPDP+ 
Sbjct: 665  MNRISRQILQETGNEPDPAT 684


>gi|220936192|ref|YP_002515091.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio
            sulfidophilus HL-EbGr7]
 gi|219997502|gb|ACL74104.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio
            sulfidophilus HL-EbGr7]
          Length = 619

 Score =  612 bits (1578), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 317/609 (52%), Positives = 433/609 (71%), Gaps = 12/609 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E   D+++L+L
Sbjct: 9    RLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGIAVHEQAPDSDSLIL 68

Query: 892  SN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            S+  +++D+D  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GEI+IAKRIE+
Sbjct: 69   SDSTVSTDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGEIKIAKRIED 128

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS-----SNNRVIKGN 1004
            GL  ++ A++  P +I  +L   DK+   E+K+ ++V   ID N       + N     +
Sbjct: 129  GLGQVLFALAHYPQSISTLLAEFDKVEAGEMKLTDLVVSFIDPNADDVPAVAANEADSAD 188

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE-GYNSESYIK 1063
             + +      +S S D   +       ++          F K+R  +E+  G+ ++ +  
Sbjct: 189  TDASASDDDSDSDSDDEDDDDTASEPEDTGPDPEEARERFTKLRAMYEEAMGFAAKKHTA 248

Query: 1064 AHNNISNEM----LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             +  +  EM    +  +   + +++L   L   + ++   E+ +++I VN+C MPR  FI
Sbjct: 249  KYRKVREEMASYFMEFKLLPRFVDQLTADLHEMVERIRMQERTVMDICVNRCNMPRKEFI 308

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
              FPENE NL W+D +TK +  +  +L  +   I  +Q+KL+ ++ +  L +++++DINR
Sbjct: 309  TAFPENETNLKWLDTQTKGKSKHAKLLAEHKDEILRIQKKLVAIEDESNLTISEIKDINR 368

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 369  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 428

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +
Sbjct: 429  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEEL 488

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            + +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+++P +AA    +   
Sbjct: 489  SERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNVMSPIEAATREGLSEA 548

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             +D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 549  TRDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 608

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 609  SEMLRSFLD 617



 Score =  597 bits (1540), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 310/596 (52%), Positives = 424/596 (71%), Gaps = 12/596 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E   D+++L+L
Sbjct: 9   RLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGIAVHEQAPDSDSLIL 68

Query: 102 SN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           S+  +++D+D  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GEI+IAKRIE+
Sbjct: 69  SDSTVSTDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGEIKIAKRIED 128

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS-----SNNRVIKGN 214
           GL  ++ A++  P +I  +L   DK+   E+K+ ++V   ID N       + N     +
Sbjct: 129 GLGQVLFALAHYPQSISTLLAEFDKVEAGEMKLTDLVVSFIDPNADDVPAVAANEADSAD 188

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE-GYNSESYIK 273
            + +      +S S D   +       ++          F K+R  +E+  G+ ++ +  
Sbjct: 189 TDASASDDDSDSDSDDEDDDDTASEPEDTGPDPEEARERFTKLRAMYEEAMGFAAKKHTA 248

Query: 274 AHNNISNEM----LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            +  +  EM    +  +   + +++L   L   + ++   E+ +++I VN+C MPR  FI
Sbjct: 249 KYRKVREEMASYFMEFKLLPRFVDQLTADLHEMVERIRMQERTVMDICVNRCNMPRKEFI 308

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
             FPENE NL W+D +TK +  +  +L  +   I  +Q+KL+ ++ +  L +++++DINR
Sbjct: 309 TAFPENETNLKWLDTQTKGKSKHAKLLAEHKDEILRIQKKLVAIEDESNLTISEIKDINR 368

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 369 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 428

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +
Sbjct: 429 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEEL 488

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           + +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+++P +AA    +   
Sbjct: 489 SERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNVMSPIEAATREGLSEA 548

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 TRDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|149376143|ref|ZP_01893908.1| sigma factor RpoD [Marinobacter algicola DG893]
 gi|149359548|gb|EDM48007.1| sigma factor RpoD [Marinobacter algicola DG893]
          Length = 616

 Score =  612 bits (1578), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 315/609 (51%), Positives = 427/609 (70%), Gaps = 6/609 (0%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D +TL
Sbjct: 7    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTL 66

Query: 890  MLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++++   T+D+       AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67   LMTDGDSTADEAAAAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 1003
            EEG++D++ A++  P     ++ A D+I +NE ++ +IV G +D +    F   +     
Sbjct: 127  EEGIRDVMAAVAHFPGITGTVIQAYDRIIENEGRLSDIVSGFLDPDGAEPFMEEDTTPDT 186

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +++     +         +      E+ ++F  +    D    +  K G   +   +
Sbjct: 187  SSTSDDSSDDDDDDDDSEEETESGPDPEETRLRFELLKEKLDAADASLAKHGRGHKKTQE 246

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A N +       +   K+ ++L + +R+  + V + E+ I++I V +C MPR  FIK FP
Sbjct: 247  ALNELGQVFAPFKLGNKAFDELVNVVRSTNDLVRENERAIMKICVRECKMPRKDFIKSFP 306

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE +L+W +  +K +  Y  ++   I  +  LQ+++ N+QT++ L ++D+++INR++  
Sbjct: 307  GNETSLDWAEKMSKGKKPYAPLIAERIDEVVRLQKRIANIQTEVDLDVSDIKEINRRVSI 366

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 547  LSGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606

Query: 1424 KIFLEGKKN 1432
            + F++ + N
Sbjct: 607  RGFIDDQGN 615



 Score =  597 bits (1539), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 416/592 (70%), Gaps = 6/592 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D +TL
Sbjct: 7   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTL 66

Query: 100 MLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++++   T+D+       AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67  LMTDGDSTADEAAAAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 213
           EEG++D++ A++  P     ++ A D+I +NE ++ +IV G +D +    F   +     
Sbjct: 127 EEGIRDVMAAVAHFPGITGTVIQAYDRIIENEGRLSDIVSGFLDPDGAEPFMEEDTTPDT 186

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +++     +         +      E+ ++F  +    D    +  K G   +   +
Sbjct: 187 SSTSDDSSDDDDDDDDSEEETESGPDPEETRLRFELLKEKLDAADASLAKHGRGHKKTQE 246

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A N +       +   K+ ++L + +R+  + V + E+ I++I V +C MPR  FIK FP
Sbjct: 247 ALNELGQVFAPFKLGNKAFDELVNVVRSTNDLVRENERAIMKICVRECKMPRKDFIKSFP 306

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE +L+W +  +K +  Y  ++   I  +  LQ+++ N+QT++ L ++D+++INR++  
Sbjct: 307 GNETSLDWAEKMSKGKKPYAPLIAERIDEVVRLQKRIANIQTEVDLDVSDIKEINRRVSI 366

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 LSGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|398937159|ref|ZP_10667198.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp.
            GM41(2012)]
 gi|398167142|gb|EJM55222.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp.
            GM41(2012)]
          Length = 616

 Score =  610 bits (1574), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/606 (52%), Positives = 427/606 (70%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  ++  I
Sbjct: 190  VKADDDTDDDDAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250  AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310  PGNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  597 bits (1538), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 311/593 (52%), Positives = 418/593 (70%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  ++  I
Sbjct: 190 VKADDDTDDDDAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250 AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310 PGNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|237803341|ref|ZP_04590926.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
            str. 1_6]
 gi|331025322|gb|EGI05378.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. oryzae
            str. 1_6]
          Length = 615

 Score =  610 bits (1573), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 318/611 (52%), Positives = 423/611 (69%), Gaps = 20/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K   ++ EE+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGDDEEEE------SADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRD 243

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 244  DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 303

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 304  FLRQFPGNEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDI 363

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 364  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 424  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 483

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 484  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 543

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 544  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 603

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 604  TRSEHLRSFLD 614



 Score =  596 bits (1537), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 312/598 (52%), Positives = 414/598 (69%), Gaps = 20/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K   ++ EE+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGDDEEEE------SADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKLGRD 243

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 244 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 303

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 304 FLRQFPGNEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDI 363

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 364 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 483

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 484 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 543

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|430762755|ref|YP_007218612.1| RNA polymerase sigma factor RpoD [Thioalkalivibrio nitratireducens
            DSM 14787]
 gi|430012379|gb|AGA35131.1| RNA polymerase sigma factor RpoD [Thioalkalivibrio nitratireducens
            DSM 14787]
          Length = 621

 Score =  610 bits (1572), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 314/618 (50%), Positives = 427/618 (69%), Gaps = 18/618 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GKE+GYLT++E+ND LP+ IID + IE II     M I+V E   D 
Sbjct: 4    EEQQSQLKELIARGKEQGYLTYTEVNDHLPDSIIDSDQIEDIIAMINDMGIAVHEQAPDA 63

Query: 887  ETLMLSNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            +TL+LS+ + S D+  E   AAL+ VDSDFGRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 64   DTLLLSDGSVSSDEDAEDAVAALAAVDSDFGRTTDPVRMYMREMGTVELLTREGEIRIAK 123

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEGL  ++ A++  P+ I ++L    ++ +N  ++ ++V   I         V +G  
Sbjct: 124  RIEEGLMQVLFALAHHPSAISQLLEQYQRLIENNTRLTDLVVSFISPEAGDGEAVARGLA 183

Query: 1006 NNNEEKILIESSSADLS---------------TEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                      +++A  S                E       E+ ++F+ ++   +  ++A
Sbjct: 184  EPGTATESPPTATAQTSDEDSDDSDADDSDEEVEDTGPDPEEARVRFARLAELHNAAQEA 243

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +++ Y  E+Y +A    +   +  +   + +++L   L   I Q+ + E+QI+++VV +
Sbjct: 244  CQRKDY--EAYARAREETARYFMEFKLVPRVVDELTSNLHATIAQIRRYERQIMQLVVAQ 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  F+  FP+NE NL+W++   K +  Y   L      +  LQ+KL+ ++    L 
Sbjct: 302  ARMPRKTFLDSFPKNETNLDWIEQAQKGKGKYTEQLAEVADEVVRLQKKLLEIEKQANLS 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE 
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEM 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A +MEMPE+KIRK+MKI+KEP+SME+P+GDDEDSHLGDFIEDE ++ P ++
Sbjct: 482  GREATPEELAERMEMPEDKIRKVMKISKEPISMETPIGDDEDSHLGDFIEDEKVMTPVES 541

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A  A +    ++IL +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542  AARAKLSEATREILATLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHP+R   L+ +++
Sbjct: 602  LRKLRHPTRAELLRTYMD 619



 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 310/605 (51%), Positives = 418/605 (69%), Gaps = 18/605 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GKE+GYLT++E+ND LP+ IID + IE II     M I+V E   D 
Sbjct: 4   EEQQSQLKELIARGKEQGYLTYTEVNDHLPDSIIDSDQIEDIIAMINDMGIAVHEQAPDA 63

Query: 97  ETLMLSNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           +TL+LS+ + S D+  E   AAL+ VDSDFGRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 64  DTLLLSDGSVSSDEDAEDAVAALAAVDSDFGRTTDPVRMYMREMGTVELLTREGEIRIAK 123

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEGL  ++ A++  P+ I ++L    ++ +N  ++ ++V   I         V +G  
Sbjct: 124 RIEEGLMQVLFALAHHPSAISQLLEQYQRLIENNTRLTDLVVSFISPEAGDGEAVARGLA 183

Query: 216 NNNEEKILIESSSADLS---------------TEQLEKLKYESLIKFSNISFHFDKMRKA 260
                     +++A  S                E       E+ ++F+ ++   +  ++A
Sbjct: 184 EPGTATESPPTATAQTSDEDSDDSDADDSDEEVEDTGPDPEEARVRFARLAELHNAAQEA 243

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +++ Y  E+Y +A    +   +  +   + +++L   L   I Q+ + E+QI+++VV +
Sbjct: 244 CQRKDY--EAYARAREETARYFMEFKLVPRVVDELTSNLHATIAQIRRYERQIMQLVVAQ 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  F+  FP+NE NL+W++   K +  Y   L      +  LQ+KL+ ++    L 
Sbjct: 302 ARMPRKTFLDSFPKNETNLDWIEQAQKGKGKYTEQLAEVADEVVRLQKKLLEIEKQANLS 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE 
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEM 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A +MEMPE+KIRK+MKI+KEP+SME+P+GDDEDSHLGDFIEDE ++ P ++
Sbjct: 482 GREATPEELAERMEMPEDKIRKVMKISKEPISMETPIGDDEDSHLGDFIEDEKVMTPVES 541

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A  A +    ++IL +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542 AARAKLSEATREILATLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 621 LRKLR 625
           LRKLR
Sbjct: 602 LRKLR 606


>gi|66047868|ref|YP_237709.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
            B728a]
 gi|424068239|ref|ZP_17805695.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. avellanae
            str. ISPaVe013]
 gi|440744098|ref|ZP_20923404.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP39023]
 gi|63258575|gb|AAY39671.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas syringae pv.
            syringae B728a]
 gi|407998580|gb|EKG38986.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. avellanae
            str. ISPaVe013]
 gi|440374554|gb|ELQ11282.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP39023]
          Length = 616

 Score =  610 bits (1572), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/611 (51%), Positives = 424/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 415/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|296932701|gb|ADH93504.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. In5]
          Length = 616

 Score =  609 bits (1570), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/606 (52%), Positives = 429/606 (70%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  +++ I
Sbjct: 190  VKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKAAI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250  AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   + +  Y   + R  P I   QQKLI LQT+  L + +++DINR+M 
Sbjct: 310  PGNEVDESWSDGLARGKGKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 311/593 (52%), Positives = 420/593 (70%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  +++ I
Sbjct: 190 VKADDDTDDEEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKAAI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250 AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   + +  Y   + R  P I   QQKLI LQT+  L + +++DINR+M 
Sbjct: 310 PGNEVDESWSDGLARGKGKYAEAIGRLQPDIIRCQQKLIALQTETGLTIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|387812955|ref|YP_005428432.1| RNA polymerase sigma factor RpoD [Marinobacter hydrocarbonoclasticus
            ATCC 49840]
 gi|381337962|emb|CCG94009.1| sigma D (sigma 70) factor of RNA polymerase [Marinobacter
            hydrocarbonoclasticus ATCC 49840]
          Length = 620

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/614 (51%), Positives = 423/614 (68%), Gaps = 14/614 (2%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 9    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 68

Query: 890  MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 69   LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 128

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +   +     G   +
Sbjct: 129  EEGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIVTGFLDPD---DAEPFMGEDTS 185

Query: 1008 NEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             E+    +S ++    +     +          E+ ++F  +    D   KA  K G   
Sbjct: 186  TEDTSADDSDASSDDDDDDTSSEDDNDNGPDPEETRLRFELLKEKLDAAEKALAKHGRGH 245

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +   +A N +       +   K+ ++L + +R+  + V + E+ I++I V  C MPR  F
Sbjct: 246  KKTQEALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDF 305

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            IK FP NE +L W       +  Y   +   +  I  LQ+++ N+QT++ L + D+++IN
Sbjct: 306  IKWFPGNETDLEWAGEIAATKKPYAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEIN 365

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 366  RRVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 425

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 426  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 485

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R 
Sbjct: 486  LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLRE 545

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              + +L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 546  ATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 605

Query: 1419 RYYKLKIFLEGKKN 1432
            R   L+ F++ + N
Sbjct: 606  RSDHLRGFIDDQGN 619



 Score =  593 bits (1530), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/597 (51%), Positives = 412/597 (69%), Gaps = 14/597 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 9   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 68

Query: 100 MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 69  LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 128

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +   +     G   +
Sbjct: 129 EEGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIVTGFLDPD---DAEPFMGEDTS 185

Query: 218 NEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
            E+    +S ++    +     +          E+ ++F  +    D   KA  K G   
Sbjct: 186 TEDTSADDSDASSDDDDDDTSSEDDNDNGPDPEETRLRFELLKEKLDAAEKALAKHGRGH 245

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +   +A N +       +   K+ ++L + +R+  + V + E+ I++I V  C MPR  F
Sbjct: 246 KKTQEALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDF 305

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           IK FP NE +L W       +  Y   +   +  I  LQ+++ N+QT++ L + D+++IN
Sbjct: 306 IKWFPGNETDLEWAGEIAATKKPYAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEIN 365

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 366 RRVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 425

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 426 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 485

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R 
Sbjct: 486 LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLRE 545

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             + +L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 546 ATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|418019755|ref|ZP_12659178.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Regiella
            insecticola R5.15]
 gi|347604885|gb|EGY29428.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Regiella
            insecticola R5.15]
          Length = 615

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 318/627 (50%), Positives = 425/627 (67%), Gaps = 40/627 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P  I  +L   D+   +E+++ +++ G +D N   N  +    
Sbjct: 123  KRIEEGINQVQCSVAEYPEAITYLLEQYDRAEADEVRLSDLITGFVDPNPKENEDI---T 179

Query: 1005 KNNNEEKILIESSSADLSTEQL---------EKLKYESLI-------KFSNISFHFDKMR 1048
             N +   I      ++LSTEQL            + +S +       KFS +   ++  +
Sbjct: 180  PNTSATHI-----GSELSTEQLIDSDDDTEGSDAENDSSVDPVLAREKFSELREQYENTK 234

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEK 1101
            KA +K+G N       H N  NE+L +       R   K  + L + +R  + Q+   E+
Sbjct: 235  KAIKKDGRN-------HPNAKNEILALSNIFKLFRLVPKQFDYLVNNMRLMMKQIRAQER 287

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
             I+++   +C MP+  F+ +   +E N  W D+    +  ++  L      +   ++KLI
Sbjct: 288  IIIKLCFEQCKMPKKIFLALSTRHETNEKWFDDALLAKKPWSEKLKEVAEDVDCCRKKLI 347

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++    L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 348  QIEEKTGLTVEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 407

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 408  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 467

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ++RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 468  VARQMLQEKGREPTPEELAEQMSMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 527

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
              +  P  +A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 528  TTLELPLGSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 587

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 588  RIRQIEAKALRKLRHPSRSEVLRSFLD 614



 Score =  594 bits (1532), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/614 (50%), Positives = 416/614 (67%), Gaps = 40/614 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P  I  +L   D+   +E+++ +++ G +D N   N  +    
Sbjct: 123 KRIEEGINQVQCSVAEYPEAITYLLEQYDRAEADEVRLSDLITGFVDPNPKENEDI---T 179

Query: 215 KNNNEEKILIESSSADLSTEQL---------EKLKYESLI-------KFSNISFHFDKMR 258
            N +   I      ++LSTEQL            + +S +       KFS +   ++  +
Sbjct: 180 PNTSATHI-----GSELSTEQLIDSDDDTEGSDAENDSSVDPVLAREKFSELREQYENTK 234

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEK 311
           KA +K+G N       H N  NE+L +       R   K  + L + +R  + Q+   E+
Sbjct: 235 KAIKKDGRN-------HPNAKNEILALSNIFKLFRLVPKQFDYLVNNMRLMMKQIRAQER 287

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 371
            I+++   +C MP+  F+ +   +E N  W D+    +  ++  L      +   ++KLI
Sbjct: 288 IIIKLCFEQCKMPKKIFLALSTRHETNEKWFDDALLAKKPWSEKLKEVAEDVDCCRKKLI 347

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            ++    L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 348 QIEEKTGLTVEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 407

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 408 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 467

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           ++RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 468 VARQMLQEKGREPTPEELAEQMSMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 527

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
             +  P  +A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 528 TTLELPLGSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 587

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 588 RIRQIEAKALRKLR 601


>gi|120553592|ref|YP_957943.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei VT8]
 gi|120323441|gb|ABM17756.1| RNA polymerase, sigma 70 subunit, RpoD [Marinobacter aquaeolei VT8]
          Length = 618

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/614 (51%), Positives = 423/614 (68%), Gaps = 14/614 (2%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 7    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 66

Query: 890  MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67   LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +   +     G   +
Sbjct: 127  EEGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIVTGFLDPD---DAEPFMGEDTS 183

Query: 1008 NEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             E+    +S ++    +     +          E+ ++F  +    D   KA  K G   
Sbjct: 184  TEDTSADDSDTSSDDDDDDTSSEDDNDNGPDPEETRLRFELLKEKLDAAEKALAKHGRGH 243

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +   +A N +       +   K+ ++L + +R+  + V + E+ I++I V  C MPR  F
Sbjct: 244  KKTQEALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDF 303

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            IK FP NE +L W       +  Y   +   +  I  LQ+++ N+QT++ L + D+++IN
Sbjct: 304  IKWFPGNETDLEWAGEIAATKKPYAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEIN 363

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 364  RRVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 423

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 424  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 483

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R 
Sbjct: 484  LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLRE 543

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              + +L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 544  ATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 603

Query: 1419 RYYKLKIFLEGKKN 1432
            R   L+ F++ + N
Sbjct: 604  RSDHLRGFIDDQGN 617



 Score =  593 bits (1530), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/597 (51%), Positives = 412/597 (69%), Gaps = 14/597 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D +TL
Sbjct: 7   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVCEETPDADTL 66

Query: 100 MLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +++  + T+D+       AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67  LMTEGDSTADEAAAAEAAAALAAVETDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           EEG++D++ A++  P T   ++ A D+I +NE +I +IV G +D +   +     G   +
Sbjct: 127 EEGIRDVMAAVAHFPGTAGTVIQAYDRIIENEGRISDIVTGFLDPD---DAEPFMGEDTS 183

Query: 218 NEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
            E+    +S ++    +     +          E+ ++F  +    D   KA  K G   
Sbjct: 184 TEDTSADDSDTSSDDDDDDTSSEDDNDNGPDPEETRLRFELLKEKLDAAEKALAKHGRGH 243

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +   +A N +       +   K+ ++L + +R+  + V + E+ I++I V  C MPR  F
Sbjct: 244 KKTQEALNELGQVFAPFKLANKAFDELVNVVRSTNDLVRENERAIMQICVRDCKMPRKDF 303

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           IK FP NE +L W       +  Y   +   +  I  LQ+++ N+QT++ L + D+++IN
Sbjct: 304 IKWFPGNETDLEWAGEIAATKKPYAAAIGERVDEIVRLQKRIQNVQTEVDLDVADIKEIN 363

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 364 RRVSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 423

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 424 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 483

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R 
Sbjct: 484 LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLRE 543

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             + +L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 ATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|257483092|ref|ZP_05637133.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
            str. ATCC 11528]
 gi|289627702|ref|ZP_06460656.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
            str. NCPPB 3681]
 gi|289649021|ref|ZP_06480364.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
            str. 2250]
 gi|416014366|ref|ZP_11562193.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. B076]
 gi|416021896|ref|ZP_11567187.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. race 4]
 gi|422406475|ref|ZP_16483503.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. race 4]
 gi|422583649|ref|ZP_16658770.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
            str. 0893_23]
 gi|422595506|ref|ZP_16669793.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. lachrymans
            str. M301315]
 gi|422607542|ref|ZP_16679540.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. mori str.
            301020]
 gi|422682334|ref|ZP_16740600.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
            str. ATCC 11528]
 gi|298160137|gb|EFI01166.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
            savastanoi NCPPB 3335]
 gi|320325995|gb|EFW82053.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. B076]
 gi|320332070|gb|EFW88006.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. race 4]
 gi|330868477|gb|EGH03186.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
            str. 0893_23]
 gi|330881700|gb|EGH15849.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. glycinea
            str. race 4]
 gi|330891182|gb|EGH23843.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. mori str.
            301020]
 gi|330985810|gb|EGH83913.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. lachrymans
            str. M301315]
 gi|331011674|gb|EGH91730.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
            str. ATCC 11528]
          Length = 616

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 315/609 (51%), Positives = 425/609 (69%), Gaps = 15/609 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSE 1059
            K    +++E+   ES+ A    +++E      +   +F  +S   +  RKA +K G + +
Sbjct: 190  KAEGTDDDEE---ESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDK 246

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
              I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F+
Sbjct: 247  HAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFL 306

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            + FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR
Sbjct: 307  RQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINR 366

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 367  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 426

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 427  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 486

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
              +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 487  GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 546

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R
Sbjct: 547  TREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 606

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 607  SEHLRSFLD 615



 Score =  594 bits (1532), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 309/596 (51%), Positives = 416/596 (69%), Gaps = 15/596 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSE 269
           K    +++E+   ES+ A    +++E      +   +F  +S   +  RKA +K G + +
Sbjct: 190 KAEGTDDDEE---ESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDK 246

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
             I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F+
Sbjct: 247 HAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFL 306

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           + FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR
Sbjct: 307 RQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINR 366

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 367 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 426

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 427 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 486

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 487 GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 546

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 TREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|410094092|ref|ZP_11290547.1| RNA polymerase sigma factor RpoD [Pseudomonas viridiflava UASWS0038]
 gi|409758505|gb|EKN43800.1| RNA polymerase sigma factor RpoD [Pseudomonas viridiflava UASWS0038]
          Length = 616

 Score =  608 bits (1568), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/611 (51%), Positives = 423/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G  
Sbjct: 190  KAEGTDDDEE-----ESADASDEEDEVESGPDPVIAAQRFGAVSDQMEITRKALKKLGRE 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  ++++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  594 bits (1531), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 414/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G  
Sbjct: 190 KAEGTDDDEE-----ESADASDEEDEVESGPDPVIAAQRFGAVSDQMEITRKALKKLGRE 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  ++++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALDRLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|422618503|ref|ZP_16687200.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
            str. M301072]
 gi|422668614|ref|ZP_16728469.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
            str. DSM 50252]
 gi|424074249|ref|ZP_17811659.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. avellanae
            str. ISPaVe037]
 gi|440721002|ref|ZP_20901412.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP34876]
 gi|440727203|ref|ZP_20907442.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP34881]
 gi|443641935|ref|ZP_21125785.1| RNA polymerase sigma factor RpoD (sig-70) [Pseudomonas syringae pv.
            syringae B64]
 gi|330898880|gb|EGH30299.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
            str. M301072]
 gi|330980978|gb|EGH79081.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
            str. DSM 50252]
 gi|407994754|gb|EKG35313.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. avellanae
            str. ISPaVe037]
 gi|440364397|gb|ELQ01529.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP34881]
 gi|440364775|gb|ELQ01897.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae BRIP34876]
 gi|443281952|gb|ELS40957.1| RNA polymerase sigma factor RpoD (sig-70) [Pseudomonas syringae pv.
            syringae B64]
          Length = 616

 Score =  608 bits (1567), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 317/611 (51%), Positives = 423/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  594 bits (1531), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 414/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + +  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAA 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|300112780|ref|YP_003759355.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299538717|gb|ADJ27034.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii C-113]
          Length = 602

 Score =  607 bits (1566), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 309/611 (50%), Positives = 436/611 (71%), Gaps = 21/611 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            ++ + + K+LI  GK+RGYL++SE+ND LPE++ID E IE II  F  M ISV E + + 
Sbjct: 7    QDRQSQLKLLIARGKDRGYLSYSEVNDHLPEEVIDPEQIEDIITMFNDMGISVHEDMAEA 66

Query: 887  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + L ++    +DD+  E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 67   DALAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAK 126

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG++ +  A+S  P ++ E+L   +K+   EI++ +++ G                 
Sbjct: 127  RIEEGMRQVYTALSRFPGSVAELLRQYEKVEVGEIRLVDVISGF---------------- 170

Query: 1006 NNNEEKILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EGYNSESY 1061
              +EE  L ES++ +   +S+E   + + ++ +    +  +F ++RK +E+ +  + +  
Sbjct: 171  QESEEADLKESAAEEEVSVSSEGNAEEENDNGLDLDRVQEYFAQLRKLYERCQAADHKGN 230

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
              A   +S   L ++   +  ++L + LR  + ++  +E+ I++I VN   MPR  F+  
Sbjct: 231  DGALEELSEYFLQLKLMPRLSQRLIENLRRVVAEIRVLERSIMKIAVNSAQMPRKDFLSS 290

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F + E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + +  +++INR +
Sbjct: 291  FQKQETNLNWVEKHIRAKKHYSSVLRKQGDAIQKAQEKLIALEQRAGMSITQIKEINRSL 350

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 351  SIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 410

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A 
Sbjct: 411  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAE 470

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            ++EMP++K+RK++KIA+EP+SME+P+GDDEDSHLGDF+ED  +++P D+A+ + +R   +
Sbjct: 471  RVEMPKDKVRKVLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQ 530

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
             IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 531  LILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 590

Query: 1422 KLKIFLEGKKN 1432
            +L+ FL+ + N
Sbjct: 591  QLRSFLDIENN 601



 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/594 (50%), Positives = 424/594 (71%), Gaps = 21/594 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           ++ + + K+LI  GK+RGYL++SE+ND LPE++ID E IE II  F  M ISV E + + 
Sbjct: 7   QDRQSQLKLLIARGKDRGYLSYSEVNDHLPEEVIDPEQIEDIITMFNDMGISVHEDMAEA 66

Query: 97  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + L ++    +DD+  E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 67  DALAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAK 126

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG++ +  A+S  P ++ E+L   +K+   EI++ +++ G                 
Sbjct: 127 RIEEGMRQVYTALSRFPGSVAELLRQYEKVEVGEIRLVDVISGF---------------- 170

Query: 216 NNNEEKILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EGYNSESY 271
             +EE  L ES++ +   +S+E   + + ++ +    +  +F ++RK +E+ +  + +  
Sbjct: 171 QESEEADLKESAAEEEVSVSSEGNAEEENDNGLDLDRVQEYFAQLRKLYERCQAADHKGN 230

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
             A   +S   L ++   +  ++L + LR  + ++  +E+ I++I VN   MPR  F+  
Sbjct: 231 DGALEELSEYFLQLKLMPRLSQRLIENLRRVVAEIRVLERSIMKIAVNSAQMPRKDFLSS 290

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F + E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + +  +++INR +
Sbjct: 291 FQKQETNLNWVEKHIRAKKHYSSVLRKQGDAIQKAQEKLIALEQRAGMSITQIKEINRSL 350

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 351 SIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 410

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A 
Sbjct: 411 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAE 470

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           ++EMP++K+RK++KIA+EP+SME+P+GDDEDSHLGDF+ED  +++P D+A+ + +R   +
Sbjct: 471 RVEMPKDKVRKVLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQ 530

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 531 LILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|422673121|ref|ZP_16732482.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
            str. M302273]
 gi|330970856|gb|EGH70922.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
            str. M302273]
          Length = 616

 Score =  607 bits (1566), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 316/611 (51%), Positives = 424/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M+++HTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTNHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/598 (51%), Positives = 415/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M+++HTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTNHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|397685696|ref|YP_006523015.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 10701]
 gi|395807252|gb|AFN76657.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 10701]
          Length = 617

 Score =  607 bits (1566), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 421/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS----------NNRVI 1001
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +               +  
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPVTPQAT 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                +++++    + S ++            + ++F  ++   D  +KA +K G  S+  
Sbjct: 190  AKPADDDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLDVAKKALKKHGRGSQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
              A   ++   + I+   K  + L   +R+ ++Q+   E+ I++I V    MPR  F++ 
Sbjct: 250  TDALQELATLFMPIKLIPKQYDALVQRVRDALSQIRAQERAIMQICVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP +E +L+W D     +  Y   +      I+  QQKLI L+ + VL + D++DINR+M
Sbjct: 310  FPNHETDLDWADQLAAGKSKYAEAIAARKEDIQSCQQKLIALEEECVLAIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 306/594 (51%), Positives = 412/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS----------NNRVI 211
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +               +  
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPVTPQAT 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
               +++++    + S ++            + ++F  ++   D  +KA +K G  S+  
Sbjct: 190 AKPADDDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLDVAKKALKKHGRGSQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
             A   ++   + I+   K  + L   +R+ ++Q+   E+ I++I V    MPR  F++ 
Sbjct: 250 TDALQELATLFMPIKLIPKQYDALVQRVRDALSQIRAQERAIMQICVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP +E +L+W D     +  Y   +      I+  QQKLI L+ + VL + D++DINR+M
Sbjct: 310 FPNHETDLDWADQLAAGKSKYAEAIAARKEDIQSCQQKLIALEEECVLAIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|422650747|ref|ZP_16713548.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. actinidiae
            str. M302091]
 gi|330963831|gb|EGH64091.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. actinidiae
            str. M302091]
          Length = 616

 Score =  607 bits (1565), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 317/611 (51%), Positives = 424/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       I    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 415/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       I    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADSSDEEDEVESGPDPIIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|407368259|ref|ZP_11114791.1| RNA polymerase sigma factor RpoD [Pseudomonas mandelii JR-1]
          Length = 616

 Score =  607 bits (1565), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 317/606 (52%), Positives = 427/606 (70%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  ++  I
Sbjct: 190  VKADDDTDDDEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250  AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310  PGNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/593 (52%), Positives = 418/593 (70%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 I----LIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           +      +   A+ ST+  E+ +       +  +F  +S   +  RKA +K G  ++  I
Sbjct: 190 VKADDDTDDDEAEASTDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKLAI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ F
Sbjct: 250 AELVLLAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310 PGNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|28867765|ref|NP_790384.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato str.
            DC3000]
 gi|213967690|ref|ZP_03395837.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382750|ref|ZP_07231168.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
            Max13]
 gi|302064027|ref|ZP_07255568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
            K40]
 gi|302130708|ref|ZP_07256698.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tomato
            NCPPB 1108]
 gi|422296553|ref|ZP_16384220.1| RNA polymerase sigma-70 factor [Pseudomonas avellanae BPIC 631]
 gi|422591085|ref|ZP_16665734.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
            morsprunorum str. M302280]
 gi|28851000|gb|AAO54079.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato str.
            DC3000]
 gi|213927466|gb|EEB61014.1| RNA polymerase sigma-70 factor [Pseudomonas syringae pv. tomato T1]
 gi|330878419|gb|EGH12568.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
            morsprunorum str. M302280]
 gi|407992237|gb|EKG33910.1| RNA polymerase sigma-70 factor [Pseudomonas avellanae BPIC 631]
          Length = 616

 Score =  607 bits (1565), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 316/611 (51%), Positives = 424/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  593 bits (1528), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/598 (51%), Positives = 415/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|407791430|ref|ZP_11138514.1| RNA polymerase sigma factor RpoD [Gallaecimonas xiamenensis 3-C-1]
 gi|407200221|gb|EKE70231.1| RNA polymerase sigma factor RpoD [Gallaecimonas xiamenensis 3-C-1]
          Length = 613

 Score =  607 bits (1564), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 423/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E   D +TLM+
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPDDIVDSDQIEDIIQMINDMGIQVFESAPDADTLMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   SEDSTDEDAVEAAAQALATVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--- 1008
              +  +++  P  I  +L   DK+   E ++ +I+ G ID N   +      +  +    
Sbjct: 128  NQVQCSVAEYPEAITYLLEQYDKVEAGEARLSDIISGFIDPNAVEDAAPTATHVGSELTQ 187

Query: 1009 ----EEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
                EE    E      S+E    L  E +  KF+ +   ++  R   + +G  S+   +
Sbjct: 188  EQQNEEDDDEEEEDNSDSSEDDNSLDPELAREKFAGLRTQYEAARTVIKAKGRASDEARE 247

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++      R   K  ++L   +R+ +++V   E+ I+++ V +  MPR  F+K FP
Sbjct: 248  EVLKLAEIFKEFRLVPKQFDRLVADMRDMMDRVRVQERLIMKLAVEEAKMPRKVFMKTFP 307

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE N+ W+D   +    Y+ ++      ++   QKL  ++ +  L +  ++DINR+M  
Sbjct: 308  GNESNMGWLDGHLEAGKGYSEVMKGLEEDLRRCVQKLQQIEQETGLTIESIKDINRRMSI 367

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +AI+M
Sbjct: 428  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAIRM 487

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S++   +++
Sbjct: 488  AMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPADAATSESLKFATQEV 547

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 548  LSSLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 607

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 608  RSFLD 612



 Score =  593 bits (1528), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 414/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E   D +TLM+
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPDDIVDSDQIEDIIQMINDMGIQVFESAPDADTLMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  SEDSTDEDAVEAAAQALATVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--- 218
             +  +++  P  I  +L   DK+   E ++ +I+ G ID N   +      +  +    
Sbjct: 128 NQVQCSVAEYPEAITYLLEQYDKVEAGEARLSDIISGFIDPNAVEDAAPTATHVGSELTQ 187

Query: 219 ----EEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
               EE    E      S+E    L  E +  KF+ +   ++  R   + +G  S+   +
Sbjct: 188 EQQNEEDDDEEEEDNSDSSEDDNSLDPELAREKFAGLRTQYEAARTVIKAKGRASDEARE 247

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++      R   K  ++L   +R+ +++V   E+ I+++ V +  MPR  F+K FP
Sbjct: 248 EVLKLAEIFKEFRLVPKQFDRLVADMRDMMDRVRVQERLIMKLAVEEAKMPRKVFMKTFP 307

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE N+ W+D   +    Y+ ++      ++   QKL  ++ +  L +  ++DINR+M  
Sbjct: 308 GNESNMGWLDGHLEAGKGYSEVMKGLEEDLRRCVQKLQQIEQETGLTIESIKDINRRMSI 367

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +AI+M
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAIRM 487

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S++   +++
Sbjct: 488 AMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPADAATSESLKFATQEV 547

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LSSLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|418294104|ref|ZP_12906005.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri ATCC 14405 =
            CCUG 16156]
 gi|379065488|gb|EHY78231.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri ATCC 14405 =
            CCUG 16156]
          Length = 617

 Score =  607 bits (1564), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 317/614 (51%), Positives = 424/614 (69%), Gaps = 24/614 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +         G     E +
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDD-------GAAGPQEVE 182

Query: 1012 ILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKMRKAFEKE 1054
                 + A  +T+  +  + +                 + ++F  ++   +K  KA +K 
Sbjct: 183  PEAPKAPAKAATDDKDDEEEDDSDSEEEEGDGGPDPEVARLRFGAVAEQLEKANKALKKH 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  S+  ++    ++   + I+   K  + L + +RN +NQ+   E+ I+++ V    MP
Sbjct: 243  GRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R  F++ FP NEINL+W D     +  Y   +      I+  QQKLI LQ +  L + D+
Sbjct: 303  RADFLRQFPNNEINLDWADQLASGKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADI 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   
Sbjct: 483  TPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVE 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHP+R   L+ FL+
Sbjct: 603  RHPTRSEHLRSFLD 616



 Score =  593 bits (1528), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/601 (51%), Positives = 415/601 (69%), Gaps = 24/601 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +         G     E +
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDD-------GAAGPQEVE 182

Query: 222 ILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKMRKAFEKE 264
                + A  +T+  +  + +                 + ++F  ++   +K  KA +K 
Sbjct: 183 PEAPKAPAKAATDDKDDEEEDDSDSEEEEGDGGPDPEVARLRFGAVAEQLEKANKALKKH 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  S+  ++    ++   + I+   K  + L + +RN +NQ+   E+ I+++ V    MP
Sbjct: 243 GRASQQAVEELEALAILFMPIKLVPKQYDALVERVRNALNQIRIQERAIMQLCVRDARMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R  F++ FP NEINL+W D     +  Y   +      I+  QQKLI LQ +  L + D+
Sbjct: 303 RADFLRQFPNNEINLDWADQLASGKGKYAEAIGNRKEDIQRCQQKLIELQQECNLAIADI 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   
Sbjct: 483 TPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVE 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|71736970|ref|YP_272918.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
            phaseolicola 1448A]
 gi|71557523|gb|AAZ36734.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
            phaseolicola 1448A]
          Length = 616

 Score =  606 bits (1563), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 315/609 (51%), Positives = 424/609 (69%), Gaps = 15/609 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL     ++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTCVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSE 1059
            K    +++E+   ES+ A    +++E      +   +F  +S   +  RKA +K G + +
Sbjct: 190  KAEGTDDDEE---ESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDK 246

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
              I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F+
Sbjct: 247  HAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFL 306

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            + FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR
Sbjct: 307  RQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINR 366

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 367  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 426

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 427  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 486

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
              +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 487  GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 546

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R
Sbjct: 547  TREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 606

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 607  SEHLRSFLD 615



 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 309/596 (51%), Positives = 415/596 (69%), Gaps = 15/596 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL     ++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTCVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSE 269
           K    +++E+   ES+ A    +++E      +   +F  +S   +  RKA +K G + +
Sbjct: 190 KAEGTDDDEE---ESADASDDEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDK 246

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
             I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F+
Sbjct: 247 HAIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFL 306

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           + FP NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR
Sbjct: 307 RQFPGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINR 366

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 367 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 426

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 427 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 486

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 487 GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 546

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 TREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|398908982|ref|ZP_10654316.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM49]
 gi|398188921|gb|EJM76209.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM49]
          Length = 615

 Score =  606 bits (1562), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 427/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 1012 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +       +        E+  +   + +I   +F  ++   +  RKA +K G N+++ I 
Sbjct: 190  VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKATIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 418/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 222 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +       +        E+  +   + +I   +F  ++   +  RKA +K G N+++ I 
Sbjct: 190 VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKATIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|339492684|ref|YP_004712977.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri ATCC 17588 =
            LMG 11199]
 gi|338800056|gb|AEJ03888.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri ATCC 17588 =
            LMG 11199]
          Length = 617

 Score =  605 bits (1560), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 423/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             K +++    D   E   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190  AKPVVDDKDDDDEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +    ++   + I+   K  + L + +R+ +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250  TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE NL+W +     +  Y   +      I+  QQKLI L+    L + D++DINR+M
Sbjct: 310  FPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 306/594 (51%), Positives = 414/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 220 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            K +++    D   E   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190 AKPVVDDKDDDDEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +    ++   + I+   K  + L + +R+ +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250 TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE NL+W +     +  Y   +      I+  QQKLI L+    L + D++DINR+M
Sbjct: 310 FPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|386019287|ref|YP_005937311.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
 gi|327479259|gb|AEA82569.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
          Length = 617

 Score =  605 bits (1560), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 423/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             K +++    D   E   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190  AKPVVDDKDDDEEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +    ++   + I+   K  + L + +R+ +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250  TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE NL+W +     +  Y   +      I+  QQKLI L+    L + D++DINR+M
Sbjct: 310  FPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 306/594 (51%), Positives = 414/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 220 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            K +++    D   E   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190 AKPVVDDKDDDEEEESDTEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +    ++   + I+   K  + L + +R+ +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250 TEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE NL+W +     +  Y   +      I+  QQKLI L+    L + D++DINR+M
Sbjct: 310 FPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELEQQCELAIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|422659022|ref|ZP_16721452.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. lachrymans
            str. M302278]
 gi|331017645|gb|EGH97701.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. lachrymans
            str. M302278]
          Length = 616

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 315/611 (51%), Positives = 423/611 (69%), Gaps = 19/611 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 1057
            K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190  KAEGADDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245  DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305  FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +MEMPE+KIRK++KI KEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485  ELGERMEMPEDKIRKVLKITKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 545  EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 604

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 605  TRSEHLRSFLD 615



 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/598 (51%), Positives = 414/598 (69%), Gaps = 19/598 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +             + + +
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYN 267
           K    +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G +
Sbjct: 190 KAEGADDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRD 244

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  
Sbjct: 245 DKHAIAELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRAD 304

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DI
Sbjct: 305 FLRQFPGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDI 364

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 365 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 424

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 425 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 484

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +MEMPE+KIRK++KI KEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++
Sbjct: 485 ELGERMEMPEDKIRKVLKITKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLK 544

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 EATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|88810991|ref|ZP_01126247.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88791530|gb|EAR22641.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 609

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 311/611 (50%), Positives = 428/611 (70%), Gaps = 14/611 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            I++ + + + LI  GKE+GYLT++E+ND LP+DI+D E IE II     M ISV E   D
Sbjct: 3    IQDQQSQIRELIARGKEQGYLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGISVHETAPD 62

Query: 886  TETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            ++TL+LS+  + +D+D  E   AAL++VD++FGRT DP++MYMREMG+VELLTR+GEIE+
Sbjct: 63   SDTLLLSDAAVATDEDEAEEAAAALASVDAEFGRTTDPVRMYMREMGTVELLTREGEIEL 122

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL------IDKNFSSN 997
            AKRIEEGL  ++ A+S+ P +   +      +    +++ EI+ G       +D    + 
Sbjct: 123  AKRIEEGLDQVLRALSAYPESARTLCSLHRHVEAGRLRLQEILAGFRGLEDELDGGADAV 182

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
            + V  G   ++E++    +++AD      + ++      F+ I    + +  A ++ G  
Sbjct: 183  D-VSVGIDGDDEDEESASNAAADSGPNPEQAVQL-----FNRIRELHEALLIALQERGSG 236

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            SE   +    + N  L ++   K I+ + + LR  + ++ + E+++  I V + GMPR  
Sbjct: 237  SEQCRELREEMGNLFLSMKLAPKVIDGMAENLRKAVERIRRAEREVTRICVKQAGMPRKE 296

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +FP  E + +WVD   +    Y+  +      + E Q  L  +Q    L ++++++I
Sbjct: 297  FITLFPGRETDPSWVDELIRADKPYSEAVAERRQMLLEAQVGLAAIQEATGLAVSEVKEI 356

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 357  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 416

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R SRQ+LQE G EP P 
Sbjct: 417  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRTSRQMLQEMGREPQPD 476

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    ++
Sbjct: 477  ELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAAVMSPVDSATREGLK 536

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 537  ESVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 596

Query: 1418 SRYYKLKIFLE 1428
            +R   L+ FL+
Sbjct: 597  TRSESLRSFLD 607



 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 305/598 (51%), Positives = 419/598 (70%), Gaps = 14/598 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           I++ + + + LI  GKE+GYLT++E+ND LP+DI+D E IE II     M ISV E   D
Sbjct: 3   IQDQQSQIRELIARGKEQGYLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGISVHETAPD 62

Query: 96  TETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           ++TL+LS+  + +D+D  E   AAL++VD++FGRT DP++MYMREMG+VELLTR+GEIE+
Sbjct: 63  SDTLLLSDAAVATDEDEAEEAAAALASVDAEFGRTTDPVRMYMREMGTVELLTREGEIEL 122

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL------IDKNFSSN 207
           AKRIEEGL  ++ A+S+ P +   +      +    +++ EI+ G       +D    + 
Sbjct: 123 AKRIEEGLDQVLRALSAYPESARTLCSLHRHVEAGRLRLQEILAGFRGLEDELDGGADAV 182

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
           + V  G   ++E++    +++AD      + ++      F+ I    + +  A ++ G  
Sbjct: 183 D-VSVGIDGDDEDEESASNAAADSGPNPEQAVQL-----FNRIRELHEALLIALQERGSG 236

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           SE   +    + N  L ++   K I+ + + LR  + ++ + E+++  I V + GMPR  
Sbjct: 237 SEQCRELREEMGNLFLSMKLAPKVIDGMAENLRKAVERIRRAEREVTRICVKQAGMPRKE 296

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +FP  E + +WVD   +    Y+  +      + E Q  L  +Q    L ++++++I
Sbjct: 297 FITLFPGRETDPSWVDELIRADKPYSEAVAERRQMLLEAQVGLAAIQEATGLAVSEVKEI 356

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 357 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 416

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R SRQ+LQE G EP P 
Sbjct: 417 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRTSRQMLQEMGREPQPD 476

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    ++
Sbjct: 477 ELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAAVMSPVDSATREGLK 536

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 537 ESVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|399522534|ref|ZP_10763197.1| RNA polymerase sigma factor rpoD [Pseudomonas pseudoalcaligenes CECT
            5344]
 gi|399109398|emb|CCH39758.1| RNA polymerase sigma factor rpoD [Pseudomonas pseudoalcaligenes CECT
            5344]
          Length = 615

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 316/605 (52%), Positives = 421/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG-------- 1003
            ++++ AI+  P T+  IL    +++    ++ EI+ G ID +  S               
Sbjct: 130  REVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEILSGYIDPDDGSVPDEAAAPVPVKEGA 189

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
                ++E+   ES   +           E+  +F+ ++   +K RKA +K G  S+  I+
Sbjct: 190  AAEASDEEEEDESGDDEEEEGDGGPDPEEAARRFTAVAEQLEKARKALKKHGRGSKQAIE 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR  F+++FP
Sbjct: 250  ELATLAELFMPIKLVPKQYDALVTKVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NEI+++W  N  K +  Y   +      I+  QQKL +L+ +  L L +++DINR+M  
Sbjct: 310  GNEIDMDWAANLAKGKAKYAEAIGALQADIQRCQQKLADLEAECNLTLAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/592 (52%), Positives = 412/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG-------- 213
           ++++ AI+  P T+  IL    +++    ++ EI+ G ID +  S               
Sbjct: 130 REVMSAIAHFPGTVDGILAEYTRVTTEGGRLAEILSGYIDPDDGSVPDEAAAPVPVKEGA 189

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
               ++E+   ES   +           E+  +F+ ++   +K RKA +K G  S+  I+
Sbjct: 190 AAEASDEEEEDESGDDEEEEGDGGPDPEEAARRFTAVAEQLEKARKALKKHGRGSKQAIE 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR  F+++FP
Sbjct: 250 ELATLAELFMPIKLVPKQYDALVTKVRDALDRLRAQERAIMQLCVRDARMPRADFLRLFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NEI+++W  N  K +  Y   +      I+  QQKL +L+ +  L L +++DINR+M  
Sbjct: 310 GNEIDMDWAANLAKGKAKYAEAIGALQADIQRCQQKLADLEAECNLTLAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|33340521|gb|AAQ14856.1| RpoD [Pseudomonas fluorescens]
          Length = 616

 Score =  605 bits (1559), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 317/618 (51%), Positives = 423/618 (68%), Gaps = 33/618 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVGAKT 189

Query: 994  ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                   +       +++EE++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190  AKADDDTDDDEAEASSDDEEEV--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238  LKKHGRGNKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L 
Sbjct: 298  ARMPRADFVRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLT 357

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358  IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478  GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538  ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHP+R   L+ FL+
Sbjct: 598  LRKLRHPTRSEHLRSFLD 615



 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 414/605 (68%), Gaps = 33/605 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVGAKT 189

Query: 204 ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
                  +       +++EE++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190 AKADDDTDDDEAEASSDDEEEV--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238 LKKHGRGNKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L 
Sbjct: 298 ARMPRADFVRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLT 357

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358 IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478 GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538 ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 621 LRKLR 625
           LRKLR
Sbjct: 598 LRKLR 602


>gi|431928756|ref|YP_007241790.1| RNA polymerase sigma-70 subunit RpoD [Pseudomonas stutzeri RCH2]
 gi|431827043|gb|AGA88160.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas stutzeri RCH2]
          Length = 617

 Score =  604 bits (1558), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 310/607 (51%), Positives = 422/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPEAPQTA 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             K   +    +   +   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190  AKPAADDKDDEDEEDSDTEEEEGDGGPDPEVARLRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            ++    ++   + I+   K  + L + +RN +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250  VEELEALAILFMPIKLVPKQYDALVERVRNALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE NL+W +     +  Y   +      I+  QQ LI L+ +  L + D++DINR+M
Sbjct: 310  FPSNETNLDWAEQLASGKGKYAEAIGNRKEDIQRCQQMLIELEQECSLAIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/594 (51%), Positives = 413/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPEAPQTA 189

Query: 220 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            K   +    +   +   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190 AKPAADDKDDEDEEDSDTEEEEGDGGPDPEVARLRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           ++    ++   + I+   K  + L + +RN +NQ+   E+ I+++ V    MPR  F++ 
Sbjct: 250 VEELEALAILFMPIKLVPKQYDALVERVRNALNQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE NL+W +     +  Y   +      I+  QQ LI L+ +  L + D++DINR+M
Sbjct: 310 FPSNETNLDWAEQLASGKGKYAEAIGNRKEDIQRCQQMLIELEQECSLAIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|398983258|ref|ZP_10689930.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM24]
 gi|398157444|gb|EJM45833.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM24]
          Length = 614

 Score =  604 bits (1557), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/600 (52%), Positives = 422/600 (70%), Gaps = 7/600 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEK 1011
             AI+  P T+  IL    +++    ++ +++ G ID +      +        K    + 
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPVEAKAAKADD 193

Query: 1012 ILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 1068
               +  +     E+  +   + +I   +F  ++   +  RKA +K G N+++ I     +
Sbjct: 194  ETDDDEAESSDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKAAIAELLAL 253

Query: 1069 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 1128
            +   + I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F++ FP NE++
Sbjct: 254  AELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVD 313

Query: 1129 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
             +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE KA
Sbjct: 314  ESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAKA 373

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 374  RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE+
Sbjct: 434  WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 493

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ LT
Sbjct: 494  KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLT 553

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL+
Sbjct: 554  AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 613



 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/587 (52%), Positives = 413/587 (70%), Gaps = 7/587 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEK 221
            AI+  P T+  IL    +++    ++ +++ G ID +      +        K    + 
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPVEAKAAKADD 193

Query: 222 ILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278
              +  +     E+  +   + +I   +F  ++   +  RKA +K G N+++ I     +
Sbjct: 194 ETDDDEAESSDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKAAIAELLAL 253

Query: 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 338
           +   + I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F++ FP NE++
Sbjct: 254 AELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVD 313

Query: 339 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
            +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE KA
Sbjct: 314 ESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAKA 373

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 374 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE+
Sbjct: 434 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 493

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ LT
Sbjct: 494 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLT 553

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|77163592|ref|YP_342117.1| hypothetical protein Noc_0045 [Nitrosococcus oceani ATCC 19707]
 gi|254436143|ref|ZP_05049650.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
 gi|76881906|gb|ABA56587.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
            19707]
 gi|207089254|gb|EDZ66526.1| Sigma-70, non-essential region family [Nitrosococcus oceani AFC27]
          Length = 602

 Score =  604 bits (1557), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 309/611 (50%), Positives = 436/611 (71%), Gaps = 21/611 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            ++ + + K+LI  GK+RGYL++SE+ND LP+D+ID E IE II  F  M ISV E + + 
Sbjct: 7    QDRQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEA 66

Query: 887  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + L ++    +DD+V E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 67   DALAIMDTAVADDEVAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAK 126

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG++ +  A+S  P ++ E+L   +K+  +EI++ +++ G                 
Sbjct: 127  RIEEGMRQVYTALSRFPGSVAELLCQYEKVEADEIRLADVISGF---------------- 170

Query: 1006 NNNEEKILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EGYNSESY 1061
              +EE  L ES++ +    S    E+ + ++ +    +   F ++R+ +E+ +  + +  
Sbjct: 171  QESEEADLKESAAEEASVSSEGSTEEEESDNGLDLDRVREQFTQLRELYERYQAADLKDN 230

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +A   +S   L ++   +  ++L + LR  + ++  +E+ I++I VN   MPR  F+  
Sbjct: 231  DRALAELSECFLQLKLVPRLSQRLIENLRGVVAEIRVLERSIMKIAVNSAQMPRKDFLSS 290

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F + E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + +  +++INR +
Sbjct: 291  FQKQETNLNWVEKHIRAKKHYSSVLRKQGDAIQKAQEKLIVLEQRAGMSITQIKEINRSL 350

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 351  SIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 410

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A 
Sbjct: 411  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAE 470

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            ++EMP++K+RK++KIA+EP+SME+P+GDDEDSHLGDF+ED  +++P D+A+ + +R   +
Sbjct: 471  RVEMPKDKVRKVLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQ 530

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
             IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 531  LILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 590

Query: 1422 KLKIFLEGKKN 1432
            +L+ FL+ + N
Sbjct: 591  QLRSFLDIENN 601



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/594 (50%), Positives = 424/594 (71%), Gaps = 21/594 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           ++ + + K+LI  GK+RGYL++SE+ND LP+D+ID E IE II  F  M ISV E + + 
Sbjct: 7   QDRQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEA 66

Query: 97  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + L ++    +DD+V E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 67  DALAIMDTAVADDEVAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEISIAK 126

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG++ +  A+S  P ++ E+L   +K+  +EI++ +++ G                 
Sbjct: 127 RIEEGMRQVYTALSRFPGSVAELLCQYEKVEADEIRLADVISGF---------------- 170

Query: 216 NNNEEKILIESSSAD---LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EGYNSESY 271
             +EE  L ES++ +    S    E+ + ++ +    +   F ++R+ +E+ +  + +  
Sbjct: 171 QESEEADLKESAAEEASVSSEGSTEEEESDNGLDLDRVREQFTQLRELYERYQAADLKDN 230

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +A   +S   L ++   +  ++L + LR  + ++  +E+ I++I VN   MPR  F+  
Sbjct: 231 DRALAELSECFLQLKLVPRLSQRLIENLRGVVAEIRVLERSIMKIAVNSAQMPRKDFLSS 290

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F + E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + +  +++INR +
Sbjct: 291 FQKQETNLNWVEKHIRAKKHYSSVLRKQGDAIQKAQEKLIVLEQRAGMSITQIKEINRSL 350

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 351 SIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 410

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A 
Sbjct: 411 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDELAE 470

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           ++EMP++K+RK++KIA+EP+SME+P+GDDEDSHLGDF+ED  +++P D+A+ + +R   +
Sbjct: 471 RVEMPKDKVRKVLKIAREPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQ 530

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 531 LILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|398853790|ref|ZP_10610382.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM80]
 gi|398238407|gb|EJN24136.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM80]
          Length = 614

 Score =  604 bits (1557), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/600 (52%), Positives = 422/600 (70%), Gaps = 7/600 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEK 1011
             AI+  P T+  IL    +++    ++ +++ G ID +      +        K    + 
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPVEAKVAKADD 193

Query: 1012 ILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 1068
               +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ I     +
Sbjct: 194  ETDDDEAESSDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRSNKATIAELLAL 253

Query: 1069 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 1128
            +   + I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F++ FP NE++
Sbjct: 254  AELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVD 313

Query: 1129 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
             +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE KA
Sbjct: 314  ESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAKA 373

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 374  RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE+
Sbjct: 434  WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 493

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ LT
Sbjct: 494  KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLT 553

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL+
Sbjct: 554  AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFLD 613



 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/587 (52%), Positives = 413/587 (70%), Gaps = 7/587 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNNNEEK 221
            AI+  P T+  IL    +++    ++ +++ G ID +      +        K    + 
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPVEAKVAKADD 193

Query: 222 ILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278
              +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ I     +
Sbjct: 194 ETDDDEAESSDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRSNKATIAELLAL 253

Query: 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 338
           +   + I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F++ FP NE++
Sbjct: 254 AELFMPIKLVPKQFEGLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEVD 313

Query: 339 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
            +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE KA
Sbjct: 314 ESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAKA 373

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 374 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE+
Sbjct: 434 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 493

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ LT
Sbjct: 494 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGLT 553

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|374369716|ref|ZP_09627738.1| sigma-70 factor [Cupriavidus basilensis OR16]
 gi|373098795|gb|EHP39894.1| sigma-70 factor [Cupriavidus basilensis OR16]
          Length = 515

 Score =  603 bits (1556), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 285/512 (55%), Positives = 393/512 (76%), Gaps = 8/512 (1%)

Query: 924  MYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKID 983
            MYMREM S  LLTR  E+EIAKRIE+GL  M+HAI++CP+TI  IL  +++++++E +ID
Sbjct: 1    MYMREMSSATLLTRKQEVEIAKRIEDGLNRMVHAIAACPSTIATILELSERVARDEARID 60

Query: 984  EIVDGLIDKNF--------SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 1035
            E+VDGLI+           +S +  +  +++ ++E +   +++    T  L KL+ + L 
Sbjct: 61   ELVDGLIEGEGDVAEAEEDTSRDEPVAEDESASDEPVDEGAAAQANETASLAKLRDDCLT 120

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            +F+ ++ HF+ MRKA+   G  SE ++ A   +  E+  IRFTAK+IE+LC  ++  + +
Sbjct: 121  RFARVANHFEAMRKAYTAHGVESEGFLVAQLAVREELKSIRFTAKTIERLCADVQTVVEE 180

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V  +E+QIL+++V +CGMPR  FI+ FP NE NL W          Y+  + R++P ++ 
Sbjct: 181  VRVVERQILQLMVERCGMPRDEFIERFPGNETNLAWGRAIAGESRSYSDSVSRSLPDLEA 240

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
             QQKLI++   +VLPL++L+ +NR+M+A E + R+AK EMT+ANLRLVISIAKKY +RG+
Sbjct: 241  YQQKLIDIHARVVLPLSELKLVNRQMLAAERQMRQAKHEMTQANLRLVISIAKKYVNRGM 300

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIET
Sbjct: 301  QFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIET 360

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISR+I+Q TG   DP+ +A +MEMPEEK+R IMKIAKEPVSME+PVG+D D+ L
Sbjct: 361  INKLNRISREIMQRTGKAADPAALAERMEMPEEKVRSIMKIAKEPVSMETPVGEDGDTSL 420

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GD I D +  +P++AAL+AS+R+ V+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQ
Sbjct: 421  GDMIADSDTASPAEAALHASLRATVREMLDDLTPREAKVLRMRFGIDMSTDYTLEEVGKQ 480

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            FDVTRERIRQIE+KA++K+RHPSR   LK FL
Sbjct: 481  FDVTRERIRQIESKAMKKMRHPSRADHLKAFL 512



 Score =  587 bits (1514), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 277/500 (55%), Positives = 385/500 (77%), Gaps = 8/500 (1%)

Query: 134 MYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKID 193
           MYMREM S  LLTR  E+EIAKRIE+GL  M+HAI++CP+TI  IL  +++++++E +ID
Sbjct: 1   MYMREMSSATLLTRKQEVEIAKRIEDGLNRMVHAIAACPSTIATILELSERVARDEARID 60

Query: 194 EIVDGLIDKNF--------SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 245
           E+VDGLI+           +S +  +  +++ ++E +   +++    T  L KL+ + L 
Sbjct: 61  ELVDGLIEGEGDVAEAEEDTSRDEPVAEDESASDEPVDEGAAAQANETASLAKLRDDCLT 120

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           +F+ ++ HF+ MRKA+   G  SE ++ A   +  E+  IRFTAK+IE+LC  ++  + +
Sbjct: 121 RFARVANHFEAMRKAYTAHGVESEGFLVAQLAVREELKSIRFTAKTIERLCADVQTVVEE 180

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V  +E+QIL+++V +CGMPR  FI+ FP NE NL W          Y+  + R++P ++ 
Sbjct: 181 VRVVERQILQLMVERCGMPRDEFIERFPGNETNLAWGRAIAGESRSYSDSVSRSLPDLEA 240

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
            QQKLI++   +VLPL++L+ +NR+M+A E + R+AK EMT+ANLRLVISIAKKY +RG+
Sbjct: 241 YQQKLIDIHARVVLPLSELKLVNRQMLAAERQMRQAKHEMTQANLRLVISIAKKYVNRGM 300

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWW+RQA+TR+IADQARTIR+PVHMIET
Sbjct: 301 QFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWWVRQAVTRAIADQARTIRVPVHMIET 360

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISR+I+Q TG   DP+ +A +MEMPEEK+R IMKIAKEPVSME+PVG+D D+ L
Sbjct: 361 INKLNRISREIMQRTGKAADPAALAERMEMPEEKVRSIMKIAKEPVSMETPVGEDGDTSL 420

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GD I D +  +P++AAL+AS+R+ V+++L+ LTPRE+KVLRMRFGI+MS+D+TLEEVGKQ
Sbjct: 421 GDMIADSDTASPAEAALHASLRATVREMLDDLTPREAKVLRMRFGIDMSTDYTLEEVGKQ 480

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIE+KA++K+R
Sbjct: 481 FDVTRERIRQIESKAMKKMR 500


>gi|345877749|ref|ZP_08829487.1| 50S ribosomal protein L3 [endosymbiont of Riftia pachyptila (vent
            Ph05)]
 gi|344225200|gb|EGV51565.1| 50S ribosomal protein L3 [endosymbiont of Riftia pachyptila (vent
            Ph05)]
          Length = 620

 Score =  603 bits (1555), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 422/607 (69%), Gaps = 14/607 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + K LI  GKE+G+LT++E+ND LPE I++ E IE I++    M I+V E   D 
Sbjct: 21   EQQRSQLKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDL 80

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            E   LS+  +TSDDD  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IA
Sbjct: 81   EDKTLSDEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIA 140

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+GLK +  A+++ P TI  +     K+ + E ++ ++++G ID N +      R  
Sbjct: 141  KRIEDGLKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVINGFIDPNETDEIPIPRPP 200

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            +   + +EE    +    D   +       E   K   +   ++ +  A +K G N+   
Sbjct: 201  RAKDSGDEE----DEEPVDTGPD-----PEEVAAKTKELGKRYNALCSALKKHGRNNPKT 251

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             KA    +   L  +    +   L  +LR+ I ++   E+ I+ + V++  MPR  FI  
Sbjct: 252  QKALEACAESFLEFKLVPNAFNHLVASLRDTIARIRAQERIIMNLCVDRARMPRKEFIAS 311

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP+NE N +W+  +      Y+  L      I   Q++LI L+ +  L ++D+++INRKM
Sbjct: 312  FPDNETNPDWLQQQLDAGKSYSEPLQEYADDIARAQKRLITLKQECQLTISDIKEINRKM 371

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A 
Sbjct: 432  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAE 491

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A +  +R   +
Sbjct: 492  RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQ 551

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 552  NMLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 611

Query: 1422 KLKIFLE 1428
            +++ FL+
Sbjct: 612  RMRSFLD 618



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/594 (52%), Positives = 412/594 (69%), Gaps = 14/594 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + K LI  GKE+G+LT++E+ND LPE I++ E IE I++    M I+V E   D 
Sbjct: 21  EQQRSQLKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDL 80

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           E   LS+  +TSDDD  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IA
Sbjct: 81  EDKTLSDEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIA 140

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+GLK +  A+++ P TI  +     K+ + E ++ ++++G ID N +      R  
Sbjct: 141 KRIEDGLKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVINGFIDPNETDEIPIPRPP 200

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           +   + +EE    +    D   +       E   K   +   ++ +  A +K G N+   
Sbjct: 201 RAKDSGDEE----DEEPVDTGPD-----PEEVAAKTKELGKRYNALCSALKKHGRNNPKT 251

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            KA    +   L  +    +   L  +LR+ I ++   E+ I+ + V++  MPR  FI  
Sbjct: 252 QKALEACAESFLEFKLVPNAFNHLVASLRDTIARIRAQERIIMNLCVDRARMPRKEFIAS 311

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP+NE N +W+  +      Y+  L      I   Q++LI L+ +  L ++D+++INRKM
Sbjct: 312 FPDNETNPDWLQQQLDAGKSYSEPLQEYADDIARAQKRLITLKQECQLTISDIKEINRKM 371

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A 
Sbjct: 432 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAE 491

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A +  +R   +
Sbjct: 492 RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQ 551

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 NMLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|440737977|ref|ZP_20917527.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens BRIP34879]
 gi|447918659|ref|YP_007399227.1| RNA polymerase sigma factor RpoD [Pseudomonas poae RE*1-1-14]
 gi|440381552|gb|ELQ18079.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens BRIP34879]
 gi|445202522|gb|AGE27731.1| RNA polymerase sigma factor RpoD [Pseudomonas poae RE*1-1-14]
          Length = 616

 Score =  603 bits (1555), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 316/606 (52%), Positives = 421/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +   +     +    +   
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1010 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
             K   E+   D      ++ + ES         +F  +S   +  RKA +K G +++  I
Sbjct: 190  PKADDETEDDDAEASSDDEDEVESGPDPVIAAQRFGAVSDQMEITRKALKKHGRSNKQAI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250  AELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M 
Sbjct: 310  PGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/593 (52%), Positives = 412/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +   +     +    +   
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 220 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 272
            K   E+   D      ++ + ES         +F  +S   +  RKA +K G +++  I
Sbjct: 190 PKADDETEDDDAEASSDDEDEVESGPDPVIAAQRFGAVSDQMEITRKALKKHGRSNKQAI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250 AELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M 
Sbjct: 310 PGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|229592968|ref|YP_002875087.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens SBW25]
 gi|229364834|emb|CAY52873.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas fluorescens
            SBW25]
          Length = 616

 Score =  603 bits (1555), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/616 (51%), Positives = 425/616 (68%), Gaps = 29/616 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 994  -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
              + ++      + + +++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190  AKADDDTEDDDAEASGDDEDEVESGPDPVIAAQ----------RFGAVSDQMEITRKALK 239

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240  KHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300  MPRTDFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360  EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480  EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540  VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHP+R   L+ FL+
Sbjct: 600  KLRHPTRSEHLRSFLD 615



 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/603 (51%), Positives = 416/603 (68%), Gaps = 29/603 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 204 -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 262
             + ++      + + +++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190 AKADDDTEDDDAEASGDDEDEVESGPDPVIAAQ----------RFGAVSDQMEITRKALK 239

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240 KHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300 MPRTDFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360 EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480 EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 623 KLR 625
           KLR
Sbjct: 600 KLR 602


>gi|302185957|ref|ZP_07262630.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
            642]
          Length = 616

 Score =  603 bits (1554), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/606 (51%), Positives = 419/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 1004
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +               K  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESYI 1062
            K    +    ES+ A    +++E      +   +F  +S   +  RKA +K G + +  I
Sbjct: 190  KAEGADDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250  AEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M 
Sbjct: 310  PGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/593 (52%), Positives = 410/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 214
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +               K  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAV 189

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESYI 272
           K    +    ES+ A    +++E      +   +F  +S   +  RKA +K G + +  I
Sbjct: 190 KAEGADDEEEESADASDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250 AEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M 
Sbjct: 310 PGNEVDESWTDALAKGKSKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|345863313|ref|ZP_08815525.1| RNA polymerase sigma factor RpoD [endosymbiont of Tevnia jerichonana
            (vent Tica)]
 gi|345125774|gb|EGW55642.1| RNA polymerase sigma factor RpoD [endosymbiont of Tevnia jerichonana
            (vent Tica)]
          Length = 603

 Score =  603 bits (1554), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 422/607 (69%), Gaps = 14/607 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + K LI  GKE+G+LT++E+ND LPE I++ E IE I++    M I+V E   D 
Sbjct: 4    EQQRSQLKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDL 63

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            E   LS+  +TSDDD  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IA
Sbjct: 64   EDKTLSDEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIA 123

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+GLK +  A+++ P TI  +     K+ + E ++ ++++G ID N +      R  
Sbjct: 124  KRIEDGLKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVINGFIDPNETDEIPIPRPP 183

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            +   + +EE    +    D   +       E   K   +   ++ +  A +K G N+   
Sbjct: 184  RAKDSGDEE----DEEPVDTGPD-----PEEVAAKTKELGKRYNALCSALKKHGRNNPKT 234

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             KA    +   L  +    +   L  +LR+ I ++   E+ I+ + V++  MPR  FI  
Sbjct: 235  QKALEACAESFLEFKLVPNAFNHLVASLRDTIARIRAQERIIMNLCVDRARMPRKEFIAS 294

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP+NE N +W+  +      Y+  L      I   Q++LI L+ +  L ++D+++INRKM
Sbjct: 295  FPDNETNPDWLQQQLDAGKSYSEPLQEYADDIARAQKRLITLKQECQLTISDIKEINRKM 354

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 355  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 414

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A 
Sbjct: 415  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAE 474

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A +  +R   +
Sbjct: 475  RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQ 534

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 535  NMLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 594

Query: 1422 KLKIFLE 1428
            +++ FL+
Sbjct: 595  RMRSFLD 601



 Score =  587 bits (1514), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/594 (52%), Positives = 412/594 (69%), Gaps = 14/594 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + K LI  GKE+G+LT++E+ND LPE I++ E IE I++    M I+V E   D 
Sbjct: 4   EQQRSQLKQLIAKGKEQGFLTYAEVNDHLPEGIVEPEQIEDIVRMINDMGITVHETAPDL 63

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           E   LS+  +TSDDD  E   AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IA
Sbjct: 64  EDKTLSDEAVTSDDDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIA 123

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+GLK +  A+++ P TI  +     K+ + E ++ ++++G ID N +      R  
Sbjct: 124 KRIEDGLKQVSAALATFPVTIEMLHSMLTKVGEGEKRMADVINGFIDPNETDEIPIPRPP 183

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           +   + +EE    +    D   +       E   K   +   ++ +  A +K G N+   
Sbjct: 184 RAKDSGDEE----DEEPVDTGPD-----PEEVAAKTKELGKRYNALCSALKKHGRNNPKT 234

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            KA    +   L  +    +   L  +LR+ I ++   E+ I+ + V++  MPR  FI  
Sbjct: 235 QKALEACAESFLEFKLVPNAFNHLVASLRDTIARIRAQERIIMNLCVDRARMPRKEFIAS 294

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP+NE N +W+  +      Y+  L      I   Q++LI L+ +  L ++D+++INRKM
Sbjct: 295 FPDNETNPDWLQQQLDAGKSYSEPLQEYADDIARAQKRLITLKQECQLTISDIKEINRKM 354

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 355 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 414

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A 
Sbjct: 415 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAE 474

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A +  +R   +
Sbjct: 475 RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVVSPVDSATSEGLREATQ 534

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 535 NMLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 588


>gi|238897855|ref|YP_002923534.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
            defensa 5AT (Acyrthosiphon pisum)]
 gi|229465612|gb|ACQ67386.1| RNA polymerase, sigma 70 (sigma D) factor [Candidatus Hamiltonella
            defensa 5AT (Acyrthosiphon pisum)]
          Length = 610

 Score =  603 bits (1554), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 316/616 (51%), Positives = 424/616 (68%), Gaps = 23/616 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIARGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEQAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T +  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTGETHDDAVEAATQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P  I  +L   D++    +++ ++++G +D N   N  V+ G 
Sbjct: 123  KRIEEGIHQVQCSVAEYPEAITYLLEQYDRVELGALRLSDLINGFVDPNIQEN--VLPGA 180

Query: 1005 KNNNEE----KILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 1059
             +   E    +I  E  S     E    +  E +  KFS +   ++  R A +++G    
Sbjct: 181  IHVGSELSDAEIDDEEDSDTSEVEDDNSIDPELAQQKFSELRAQYESTRTAIKQKG---- 236

Query: 1060 SYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
               + H   + E+L +           K  + L  ++R+ +++V   E+ IL++ V +C 
Sbjct: 237  ---RHHLTTATEILKLAEIFKQFSLVPKQFDYLVSSMRSMMDRVRVQERLILKLCVEQCK 293

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MP+ +FI++F  NE N +W+     ++  +   L   +  ++   QKL  ++ +  L + 
Sbjct: 294  MPKKNFIELFLNNETNNSWLKTALAMKKPWVEKLNDVLEDVQSNVQKLRQIEEETGLSIE 353

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354  QVKDINRRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G 
Sbjct: 414  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGR 473

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +A +M MPEEKIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A 
Sbjct: 474  EPAPEELAERMLMPEEKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSAT 533

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            + S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534  SESLRLATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   LK FL+
Sbjct: 594  KLRHPSRSDVLKSFLD 609



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/603 (51%), Positives = 415/603 (68%), Gaps = 23/603 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIARGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEQAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T +  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTGETHDDAVEAATQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P  I  +L   D++    +++ ++++G +D N   N  V+ G 
Sbjct: 123 KRIEEGIHQVQCSVAEYPEAITYLLEQYDRVELGALRLSDLINGFVDPNIQEN--VLPGA 180

Query: 215 KNNNEE----KILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 269
            +   E    +I  E  S     E    +  E +  KFS +   ++  R A +++G    
Sbjct: 181 IHVGSELSDAEIDDEEDSDTSEVEDDNSIDPELAQQKFSELRAQYESTRTAIKQKG---- 236

Query: 270 SYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
              + H   + E+L +           K  + L  ++R+ +++V   E+ IL++ V +C 
Sbjct: 237 ---RHHLTTATEILKLAEIFKQFSLVPKQFDYLVSSMRSMMDRVRVQERLILKLCVEQCK 293

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MP+ +FI++F  NE N +W+     ++  +   L   +  ++   QKL  ++ +  L + 
Sbjct: 294 MPKKNFIELFLNNETNNSWLKTALAMKKPWVEKLNDVLEDVQSNVQKLRQIEEETGLSIE 353

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
            ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354 QVKDINRRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G 
Sbjct: 414 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGR 473

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +A +M MPEEKIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A 
Sbjct: 474 EPAPEELAERMLMPEEKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSAT 533

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           + S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534 SESLRLATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 623 KLR 625
           KLR
Sbjct: 594 KLR 596


>gi|388468755|ref|ZP_10142965.1| RNA polymerase sigma factor RpoD [Pseudomonas synxantha BG33R]
 gi|388012335|gb|EIK73522.1| RNA polymerase sigma factor RpoD [Pseudomonas synxantha BG33R]
          Length = 616

 Score =  603 bits (1554), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/616 (51%), Positives = 426/616 (69%), Gaps = 29/616 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 994  -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
              + ++      + +++++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190  AKADDDAEDDDAEASSDDEDEVESGPDPIVAAQ----------RFGAVSDQMEITRKALK 239

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240  KHGRSNKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300  MPRTDFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360  EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480  EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540  VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHP+R   L+ FL+
Sbjct: 600  KLRHPTRSEHLRSFLD 615



 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/603 (51%), Positives = 417/603 (69%), Gaps = 29/603 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 204 -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 262
             + ++      + +++++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190 AKADDDAEDDDAEASSDDEDEVESGPDPIVAAQ----------RFGAVSDQMEITRKALK 239

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240 KHGRSNKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300 MPRTDFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360 EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480 EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 623 KLR 625
           KLR
Sbjct: 600 KLR 602


>gi|398875235|ref|ZP_10630413.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM67]
 gi|398883031|ref|ZP_10637992.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM60]
 gi|398197604|gb|EJM84580.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM60]
 gi|398208165|gb|EJM94903.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM67]
          Length = 615

 Score =  603 bits (1554), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 426/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N+++ I 
Sbjct: 190  VKADDDTDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKAAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 417/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N+++ I 
Sbjct: 190 VKADDDTDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKAAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|54307643|ref|YP_128663.1| RNA polymerase sigma factor RpoD [Photobacterium profundum SS9]
 gi|46912066|emb|CAG18861.1| putative DNA-directed RNA polymerase, sigmasubunit [Photobacterium
            profundum SS9]
          Length = 612

 Score =  602 bits (1553), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 311/609 (51%), Positives = 420/609 (68%), Gaps = 7/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + +M++   +DDD  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DEIMMTEDNTDDDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G ID N          +  
Sbjct: 123  IEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDIISGFIDPNEEQTAAPTATHIG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 1059
            +   +  +     +L T+  ++ + ++ I       KF  +   ++KM  A    G ++ 
Sbjct: 183  SELSETDLADEDKNLETDDDDEEEEDTGIDPELAREKFLELRHSYEKMALAINTHGRHNA 242

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            +   A   +S      R   K  +KL  +LR+ +++V   E+ I+ + ++   MP+  FI
Sbjct: 243  TTEVAVGELSEIFKQFRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCIDNSKMPKKTFI 302

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            K F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+R
Sbjct: 303  KFFAGNESSPDWIDEALNSGKPYAERLKNYEEDLRRSSLKLRILEKETGLSIERIKDISR 362

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEEL 482

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   ++R+ 
Sbjct: 483  AERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAA 542

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 543  TNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 602

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 603  SDVLRSFLD 611



 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/596 (51%), Positives = 411/596 (68%), Gaps = 7/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + +M++   +DDD  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DEIMMTEDNTDDDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G ID N          +  
Sbjct: 123 IEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDIISGFIDPNEEQTAAPTATHIG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 269
           +   +  +     +L T+  ++ + ++ I       KF  +   ++KM  A    G ++ 
Sbjct: 183 SELSETDLADEDKNLETDDDDEEEEDTGIDPELAREKFLELRHSYEKMALAINTHGRHNA 242

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           +   A   +S      R   K  +KL  +LR+ +++V   E+ I+ + ++   MP+  FI
Sbjct: 243 TTEVAVGELSEIFKQFRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCIDNSKMPKKTFI 302

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           K F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+R
Sbjct: 303 KFFAGNESSPDWIDEALNSGKPYAERLKNYEEDLRRSSLKLRILEKETGLSIERIKDISR 362

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEEL 482

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   ++R+ 
Sbjct: 483 AERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAA 542

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 TNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|408479352|ref|ZP_11185571.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. R81]
          Length = 616

 Score =  602 bits (1553), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/616 (51%), Positives = 424/616 (68%), Gaps = 29/616 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 994  -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
              + ++      + + +++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190  AKADDDTEDDDAEASGDDEDEVESGPDPIIAAQ----------RFGAVSDQMEITRKALK 239

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240  KHGRANKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300  MPRADFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360  EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480  EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540  VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHP+R   L+ FL+
Sbjct: 600  KLRHPTRSEHLRSFLD 615



 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/603 (51%), Positives = 415/603 (68%), Gaps = 29/603 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 204 -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 262
             + ++      + + +++  +ES    +   Q          +F  +S   +  RKA +
Sbjct: 190 AKADDDTEDDDAEASGDDEDEVESGPDPIIAAQ----------RFGAVSDQMEITRKALK 239

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    
Sbjct: 240 KHGRANKQAIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDAR 299

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + 
Sbjct: 300 MPRADFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIA 359

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 360 EIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 419

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 420 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 479

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A 
Sbjct: 480 EPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVAT 539

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 623 KLR 625
           KLR
Sbjct: 600 KLR 602


>gi|167031434|ref|YP_001666665.1| RNA polymerase sigma factor RpoD [Pseudomonas putida GB-1]
 gi|166857922|gb|ABY96329.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida GB-1]
          Length = 616

 Score =  602 bits (1553), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/606 (51%), Positives = 422/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++   +      S +  E+ +       +  +F  +S       K  +K G   +  I
Sbjct: 190  AAKEESDDEEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRGHKESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/593 (51%), Positives = 413/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++   +      S +  E+ +       +  +F  +S       K  +K G   +  I
Sbjct: 190 AAKEESDDEEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRGHKESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|452748449|ref|ZP_21948228.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri NF13]
 gi|452007623|gb|EMD99876.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri NF13]
          Length = 617

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 310/607 (51%), Positives = 422/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             K   +    +   +   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190  AKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            ++    ++   + I+   K  + L + +RN ++Q+   E+ I+++ V    MPR  F++ 
Sbjct: 250  VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE NL+W +     +  Y   +      I   QQKLI L+ +  L + D++DINR+M
Sbjct: 310  FPNNETNLDWAEQLASGKGKYAEAIGNRKEDIVRCQQKLIELEQECDLAIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/594 (51%), Positives = 413/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAAPQEVEPETPQTT 189

Query: 220 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            K   +    +   +   + +          + ++F  ++   +K  KA +K G  S+  
Sbjct: 190 AKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARVRFGAVAEQLEKANKALKKHGRASQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           ++    ++   + I+   K  + L + +RN ++Q+   E+ I+++ V    MPR  F++ 
Sbjct: 250 VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE NL+W +     +  Y   +      I   QQKLI L+ +  L + D++DINR+M
Sbjct: 310 FPNNETNLDWAEQLASGKGKYAEAIGNRKEDIVRCQQKLIELEQECDLAIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|398866831|ref|ZP_10622305.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM78]
 gi|398238844|gb|EJN24565.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM78]
          Length = 615

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/601 (52%), Positives = 426/601 (70%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML++  
Sbjct: 14   LIKLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDTKTAKAD 193

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  ++   +  RKA +K G +++  I     
Sbjct: 194  DDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKLAIAELLA 253

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254  LADLFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314  DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 554  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 613

Query: 1428 E 1428
            +
Sbjct: 614  D 614



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/588 (52%), Positives = 417/588 (70%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML++  
Sbjct: 14  LIKLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDTKTAKAD 193

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  ++   +  RKA +K G +++  I     
Sbjct: 194 DDSDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKLAIAELLA 253

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254 LADLFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314 DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|26987129|ref|NP_742554.1| RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|148545673|ref|YP_001265775.1| RNA polymerase sigma factor RpoD [Pseudomonas putida F1]
 gi|386010046|ref|YP_005928323.1| protein RpoD [Pseudomonas putida BIRD-1]
 gi|397694925|ref|YP_006532806.1| RNA polymerase sigma factor rpoD [Pseudomonas putida DOT-T1E]
 gi|421524961|ref|ZP_15971582.1| RNA polymerase sigma factor RpoD [Pseudomonas putida LS46]
 gi|24981760|gb|AAN66018.1|AE016231_1 RNA polymerase sigma factor RpoD [Pseudomonas putida KT2440]
 gi|2654492|gb|AAB87749.1| DNA-directed RNA polymerase sigma subunit [Pseudomonas putida]
 gi|2731762|gb|AAC38073.1| sigma-70 [Pseudomonas putida]
 gi|148509731|gb|ABQ76591.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida F1]
 gi|313496752|gb|ADR58118.1| RpoD [Pseudomonas putida BIRD-1]
 gi|397331655|gb|AFO48014.1| RNA polymerase sigma factor rpoD [Pseudomonas putida DOT-T1E]
 gi|402751424|gb|EJX11937.1| RNA polymerase sigma factor RpoD [Pseudomonas putida LS46]
          Length = 616

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/606 (51%), Positives = 420/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 1010 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
                      + S    ++ + ES         +F  +S       K  +K G N +  I
Sbjct: 190  AAKEESDDDEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRNHKESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKNAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/593 (51%), Positives = 411/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 220 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 272
                     + S    ++ + ES         +F  +S       K  +K G N +  I
Sbjct: 190 AAKEESDDDEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRNHKESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKNAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|344941331|ref|ZP_08780619.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
            SV96]
 gi|344262523|gb|EGW22794.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
            SV96]
          Length = 602

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 318/600 (53%), Positives = 419/600 (69%), Gaps = 15/600 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 893
            LI  GK +GYLT++E+ND LP DI+D E IE II     M I V E   D ++L+  +  
Sbjct: 13   LIAKGKVQGYLTYAEVNDHLPSDIVDPEQIEDIIGMINDMGIQVYEVAPDEDSLITDSAA 72

Query: 894  -ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
              T D+D EE   AAL++VDS+FGRT DP++MYMREMGSVELLTR  E++IAKRIEEG +
Sbjct: 73   VTTDDEDAEEV--AALASVDSEFGRTTDPVRMYMREMGSVELLTRADELKIAKRIEEGQQ 130

Query: 953  DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++ AI+     + + L + D IS  E  I++ +++ G +D +    + V     + + E
Sbjct: 131  QLVKAIARSCIVVEDFLQSFDNISGEEGGIRLTDLISGFVDLS-EPEDFVTALPVSEDVE 189

Query: 1011 KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 1070
            +   E     L+ E++ K K E+L K             A +K GY+++   K    +++
Sbjct: 190  ETPAEEEPKGLNYEEV-KEKVEALRK------QLKTAAAAIKKHGYSNDKTDKEFEALAD 242

Query: 1071 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 1130
              +  ++T + ++KL   + N +  V + EK I++I +N   MPR  FI  FPE+E +  
Sbjct: 243  LFMEFKWTPQYLKKLTAIIPNGVTAVREQEKLIMDICINYAKMPRKEFIASFPEHETSSE 302

Query: 1131 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 1190
            W D        Y+  L      +++ Q+ L +++ +  L ++ L+DINR+M  GE KAR+
Sbjct: 303  WFDQYLNAGSKYSETLKEREKEVRKAQKILADIEAEYGLTISGLKDINRRMSIGEAKARR 362

Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
            AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 363  AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 422

Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
            IRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A +MEMPE+K+
Sbjct: 423  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAERMEMPEDKV 482

Query: 1311 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 1370
            RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P +AA  A +R   +++L  LT R
Sbjct: 483  RKVLKIAKEPISMETPIGDDEDSHLGDFIEDAKVLSPVEAATIAGLRESTQNVLAGLTAR 542

Query: 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            E+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ FL+G+
Sbjct: 543  EAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRCFLDGE 602



 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/585 (52%), Positives = 407/585 (69%), Gaps = 15/585 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 103
           LI  GK +GYLT++E+ND LP DI+D E IE II     M I V E   D ++L+  +  
Sbjct: 13  LIAKGKVQGYLTYAEVNDHLPSDIVDPEQIEDIIGMINDMGIQVYEVAPDEDSLITDSAA 72

Query: 104 -ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
             T D+D EE   AAL++VDS+FGRT DP++MYMREMGSVELLTR  E++IAKRIEEG +
Sbjct: 73  VTTDDEDAEEV--AALASVDSEFGRTTDPVRMYMREMGSVELLTRADELKIAKRIEEGQQ 130

Query: 163 DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++ AI+     + + L + D IS  E  I++ +++ G +D +    + V     + + E
Sbjct: 131 QLVKAIARSCIVVEDFLQSFDNISGEEGGIRLTDLISGFVDLS-EPEDFVTALPVSEDVE 189

Query: 221 KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 280
           +   E     L+ E++ K K E+L K             A +K GY+++   K    +++
Sbjct: 190 ETPAEEEPKGLNYEEV-KEKVEALRK------QLKTAAAAIKKHGYSNDKTDKEFEALAD 242

Query: 281 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 340
             +  ++T + ++KL   + N +  V + EK I++I +N   MPR  FI  FPE+E +  
Sbjct: 243 LFMEFKWTPQYLKKLTAIIPNGVTAVREQEKLIMDICINYAKMPRKEFIASFPEHETSSE 302

Query: 341 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 400
           W D        Y+  L      +++ Q+ L +++ +  L ++ L+DINR+M  GE KAR+
Sbjct: 303 WFDQYLNAGSKYSETLKEREKEVRKAQKILADIEAEYGLTISGLKDINRRMSIGEAKARR 362

Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
           AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 363 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 422

Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
           IRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A +MEMPE+K+
Sbjct: 423 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAERMEMPEDKV 482

Query: 521 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 580
           RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P +AA  A +R   +++L  LT R
Sbjct: 483 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDAKVLSPVEAATIAGLRESTQNVLAGLTAR 542

Query: 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           E+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 EAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 587


>gi|330812146|ref|YP_004356608.1| RNA polymerase sigma-70 factor [Pseudomonas brassicacearum subsp.
            brassicacearum NFM421]
 gi|423699702|ref|ZP_17674192.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Q8r1-96]
 gi|327380254|gb|AEA71604.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
            subsp. brassicacearum NFM421]
 gi|387996380|gb|EIK57710.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Q8r1-96]
          Length = 615

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 422/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10   RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--------IKG 1003
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
             K +++       +S D    +       +  +F  ++   +  RKA +K G N++  I 
Sbjct: 190  VKADDDTDDDEAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEVDESWTDALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/592 (52%), Positives = 413/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10  RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--------IKG 213
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
            K +++       +S D    +       +  +F  ++   +  RKA +K G N++  I 
Sbjct: 190 VKADDDTDDDEAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEVDESWTDALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|398841882|ref|ZP_10599088.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM102]
 gi|398856703|ref|ZP_10612421.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM79]
 gi|398901145|ref|ZP_10650096.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM50]
 gi|398107246|gb|EJL97252.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM102]
 gi|398180264|gb|EJM67850.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM50]
 gi|398242675|gb|EJN28282.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM79]
          Length = 615

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 424/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +  + D   E  +  +          +  +F  ++   +  RKA +K G  ++  I 
Sbjct: 190  VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRGNKLAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELIALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 415/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +  + D   E  +  +          +  +F  ++   +  RKA +K G  ++  I 
Sbjct: 190 VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRGNKLAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELIALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|395495223|ref|ZP_10426802.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. PAMC 25886]
          Length = 616

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 316/618 (51%), Positives = 417/618 (67%), Gaps = 33/618 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 994  ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                   +        ++EE++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190  AKADDDTDDDEAEASTDDEEEV--ESGPDPIIAAQ----------RFGAVSDQMELARKA 237

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +K G  S+        ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238  LKKHGRGSKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  F++ FP NE++ +W D   K +  Y   + R    I   QQKL  LQT+  L 
Sbjct: 298  ARMPRADFLRQFPGNEVDESWTDALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLT 357

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358  IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478  GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538  ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHP+R   L+ FL+
Sbjct: 598  LRKLRHPTRSEHLRSFLD 615



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/605 (51%), Positives = 408/605 (67%), Gaps = 33/605 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 204 ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
                  +        ++EE++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190 AKADDDTDDDEAEASTDDEEEV--ESGPDPIIAAQ----------RFGAVSDQMELARKA 237

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +K G  S+        ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238 LKKHGRGSKQATAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  F++ FP NE++ +W D   K +  Y   + R    I   QQKL  LQT+  L 
Sbjct: 298 ARMPRADFLRQFPGNEVDESWTDALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLT 357

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358 IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478 GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538 ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 621 LRKLR 625
           LRKLR
Sbjct: 598 LRKLR 602


>gi|395796283|ref|ZP_10475581.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Ag1]
 gi|421139627|ref|ZP_15599661.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens BBc6R8]
 gi|395339585|gb|EJF71428.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Ag1]
 gi|404509199|gb|EKA23135.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens BBc6R8]
          Length = 616

 Score =  602 bits (1552), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 315/606 (51%), Positives = 420/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      +       +   
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEIPPPIDAKA 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
             +     +   A+ ST+  E+++       +  +F  +S   +  RKA +K G  S+   
Sbjct: 190  AKADDDTDDDEAEASTDDEEEVESGPDPIIAAQRFGAVSDQMELARKALKKHGRGSKQAT 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250  AELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE++ +W D   K +  Y   + R    I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310  PGNEVDESWTDALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/593 (52%), Positives = 411/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      +       +   
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEIPPPIDAKA 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
            +     +   A+ ST+  E+++       +  +F  +S   +  RKA +K G  S+   
Sbjct: 190 AKADDDTDDDEAEASTDDEEEVESGPDPIIAAQRFGAVSDQMELARKALKKHGRGSKQAT 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ F
Sbjct: 250 AELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLRQF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE++ +W D   K +  Y   + R    I   QQKL  LQT+  L + +++DINR+M 
Sbjct: 310 PGNEVDESWTDALAKGKSKYAEAIGRFQADIVRCQQKLTALQTETGLTIAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|398873128|ref|ZP_10628393.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM74]
 gi|398200413|gb|EJM87325.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM74]
          Length = 615

 Score =  602 bits (1551), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 426/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMSAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N+++ I 
Sbjct: 190  VKADDDTDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKAAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKGKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 417/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMSAIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N+++ I 
Sbjct: 190 VKADDDTDDDDAEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRNNKAAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKGKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|398981207|ref|ZP_10689391.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM25]
 gi|398133925|gb|EJM23106.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM25]
          Length = 615

 Score =  602 bits (1551), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 314/601 (52%), Positives = 422/601 (70%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-----GNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +        +       K    +
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPIDAKAAKAD 193

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  ++   +  RKA +K G N+++ I     
Sbjct: 194  DDSEDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKAAIAELLA 253

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254  LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314  DESWSDALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 554  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 613

Query: 1428 E 1428
            +
Sbjct: 614  D 614



 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/588 (52%), Positives = 413/588 (70%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-----GNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +        +       K    +
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPIDAKAAKAD 193

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  ++   +  RKA +K G N+++ I     
Sbjct: 194 DDSEDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKAAIAELLA 253

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254 LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314 DESWSDALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|226946707|ref|YP_002801780.1| RNA polymerase sigma factor RpoD [Azotobacter vinelandii DJ]
 gi|226721634|gb|ACO80805.1| RNA polymerase sigma factor, sigma70; RpoD [Azotobacter vinelandii
            DJ]
          Length = 620

 Score =  601 bits (1549), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 317/616 (51%), Positives = 424/616 (68%), Gaps = 25/616 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   DT+ L+L
Sbjct: 10   RIKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDTDALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +I+ G ID +  S            E  
Sbjct: 130  REVMSAIAHFPGTVDGILAEYQRVTSEGGRLSDILSGYIDPDDDS------AVPAEAEVP 183

Query: 1012 ILIESSSADLSTEQLEKLKYESLI-------------------KFSNISFHFDKMRKAFE 1052
            + ++S SA       ++ + ES                     +F  ++    + R A E
Sbjct: 184  VDLKSKSAATPAASEDEDEDESEESDSDDEEGDGGPDPEIARQRFGAVAEQLGRTRVALE 243

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            + G +S   ++A   +++  + I+   K  + L + +R+ + +V   E+ I+++ V    
Sbjct: 244  RHGRHSVEGLEALQALASLFMPIKLVPKQYDTLVEQVRDALTRVRAQERAIMQLCVRDAR 303

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F++ FP NE + +WVD   K +  Y   L      IK+ QQKLI+L+  + L + 
Sbjct: 304  MPRADFLRQFPGNETDQDWVDLLAKGKAKYAEALGNLADDIKQCQQKLIDLEQKVGLTIA 363

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 364  EIKDINRQMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 423

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 424  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 483

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A 
Sbjct: 484  EPTPEELGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVAT 543

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 544  VESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FL+
Sbjct: 604  KLRHPSRSEHLRSFLD 619



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/603 (51%), Positives = 415/603 (68%), Gaps = 25/603 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   DT+ L+L
Sbjct: 10  RIKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDTDALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +I+ G ID +  S            E  
Sbjct: 130 REVMSAIAHFPGTVDGILAEYQRVTSEGGRLSDILSGYIDPDDDS------AVPAEAEVP 183

Query: 222 ILIESSSADLSTEQLEKLKYESLI-------------------KFSNISFHFDKMRKAFE 262
           + ++S SA       ++ + ES                     +F  ++    + R A E
Sbjct: 184 VDLKSKSAATPAASEDEDEDESEESDSDDEEGDGGPDPEIARQRFGAVAEQLGRTRVALE 243

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           + G +S   ++A   +++  + I+   K  + L + +R+ + +V   E+ I+++ V    
Sbjct: 244 RHGRHSVEGLEALQALASLFMPIKLVPKQYDTLVEQVRDALTRVRAQERAIMQLCVRDAR 303

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F++ FP NE + +WVD   K +  Y   L      IK+ QQKLI+L+  + L + 
Sbjct: 304 MPRADFLRQFPGNETDQDWVDLLAKGKAKYAEALGNLADDIKQCQQKLIDLEQKVGLTIA 363

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 364 EIKDINRQMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 423

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 424 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 483

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A 
Sbjct: 484 EPTPEELGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVAT 543

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 544 VESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 623 KLR 625
           KLR
Sbjct: 604 KLR 606


>gi|374703429|ref|ZP_09710299.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. S9]
          Length = 614

 Score =  601 bits (1549), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 312/604 (51%), Positives = 420/604 (69%), Gaps = 7/604 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 1004
            ++++ AI+  P T+  IL   ++++    ++ E++ G ID +        ++     + +
Sbjct: 130  REVMGAIAHFPGTVDSILAEYNRVTTEGGRLVEVLSGYIDPDDGTLPAETAAPTPAKEDS 189

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
             ++ ++    +    +           E+L +F+ ++   +   KA +K G  S+     
Sbjct: 190  ADDKDDDDDSDDGDDEEEEGDGGPDPEEALRRFTAVAEQLEIANKALKKHGRGSKQANVE 249

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
               ++   + I+   K  E L   LR+ + ++   E+ I++I V    MPR  F++ FP 
Sbjct: 250  LKALAELFMPIKLVPKQYEALVVRLRDALARLRGQERAIMQICVRDARMPRADFLRQFPG 309

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NEI+ +W +N  K +  Y   +   +  I+  QQKL+ LQ +  L L +++DINR+M  G
Sbjct: 310  NEIDESWAENLAKGKAKYAEAIGNRVADIQRCQQKLVALQAECDLTLAEIKDINRRMSIG 369

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 370  EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 429

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQAR IRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 430  TYATWWIRQAITRSIADQARAIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 489

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L
Sbjct: 490  MPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 549

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
            + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+
Sbjct: 550  SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLR 609

Query: 1425 IFLE 1428
             FL+
Sbjct: 610  SFLD 613



 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/591 (51%), Positives = 411/591 (69%), Gaps = 7/591 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 214
           ++++ AI+  P T+  IL   ++++    ++ E++ G ID +        ++     + +
Sbjct: 130 REVMGAIAHFPGTVDSILAEYNRVTTEGGRLVEVLSGYIDPDDGTLPAETAAPTPAKEDS 189

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
            ++ ++    +    +           E+L +F+ ++   +   KA +K G  S+     
Sbjct: 190 ADDKDDDDDSDDGDDEEEEGDGGPDPEEALRRFTAVAEQLEIANKALKKHGRGSKQANVE 249

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
              ++   + I+   K  E L   LR+ + ++   E+ I++I V    MPR  F++ FP 
Sbjct: 250 LKALAELFMPIKLVPKQYEALVVRLRDALARLRGQERAIMQICVRDARMPRADFLRQFPG 309

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NEI+ +W +N  K +  Y   +   +  I+  QQKL+ LQ +  L L +++DINR+M  G
Sbjct: 310 NEIDESWAENLAKGKAKYAEAIGNRVADIQRCQQKLVALQAECDLTLAEIKDINRRMSIG 369

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 370 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 429

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQAR IRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 430 TYATWWIRQAITRSIADQARAIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 489

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L
Sbjct: 490 MPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 549

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|398924270|ref|ZP_10661087.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM48]
 gi|398173601|gb|EJM61431.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM48]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 426/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 1012 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +       +        E+  +   + +I   +F  ++   +  RKA +K G ++++ I 
Sbjct: 190  VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 417/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 222 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +       +        E+  +   + +I   +F  ++   +  RKA +K G ++++ I 
Sbjct: 190 VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|398959154|ref|ZP_10677970.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM33]
 gi|426411848|ref|YP_007031947.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. UW4]
 gi|398145529|gb|EJM34310.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM33]
 gi|426270065|gb|AFY22142.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. UW4]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 427/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 1012 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +       +        E+  +   + +I   +F  ++   +  RKA +K G ++++ I 
Sbjct: 190  VKADDDTDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 418/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 222 I-----LIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +       +        E+  +   + +I   +F  ++   +  RKA +K G ++++ I 
Sbjct: 190 VKADDDTDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIVRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|90411915|ref|ZP_01219923.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90327173|gb|EAS43545.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 612

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/609 (51%), Positives = 421/609 (69%), Gaps = 7/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + +M++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DEIMMTEDNTDEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G ID N          +  
Sbjct: 123  IEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDIISGFIDPNEEQTAAPTATHIG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 1059
            +   +  +     +L T++ ++ + ++ I       KF  +   ++KM  A    G ++ 
Sbjct: 183  SELSETDLADEDKNLETDEDDEEEEDTGIDPELAREKFLELRHSYEKMALAINTHGRHNA 242

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            +   A   +S      R   K  +KL  +LR+ +++V   E+ I+ + V+   MP+  FI
Sbjct: 243  TTEVAVGELSEIFKQFRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFI 302

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            K F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+R
Sbjct: 303  KFFAGNESSPDWIDEALNSGKPYAERLKIYEEDLRRSSLKLRILEKETGLSIERIKDISR 362

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEEL 482

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   ++R+ 
Sbjct: 483  AERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAA 542

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 543  TNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 602

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 603  SDVLRSFLD 611



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 304/596 (51%), Positives = 412/596 (69%), Gaps = 7/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + +M++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DEIMMTEDNTDEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G ID N          +  
Sbjct: 123 IEDGINQVQCSVAEYPSAISYLLEQFDKVEADELRLTDIISGFIDPNEEQTAAPTATHIG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 269
           +   +  +     +L T++ ++ + ++ I       KF  +   ++KM  A    G ++ 
Sbjct: 183 SELSETDLADEDKNLETDEDDEEEEDTGIDPELAREKFLELRHSYEKMALAINTHGRHNA 242

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           +   A   +S      R   K  +KL  +LR+ +++V   E+ I+ + V+   MP+  FI
Sbjct: 243 TTEVAVGELSEIFKQFRLIPKQFDKLVRSLRDSMDKVRTNERLIMRMCVDNSKMPKKTFI 302

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           K F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+R
Sbjct: 303 KFFAGNESSPDWIDEALNSGKPYAERLKIYEEDLRRSSLKLRILEKETGLSIERIKDISR 362

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPIPEEL 482

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   ++R+ 
Sbjct: 483 AERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLQLPMDAATATNLRAA 542

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 TNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|378953250|ref|YP_005210738.1| protein RpoD [Pseudomonas fluorescens F113]
 gi|359763264|gb|AEV65343.1| RpoD [Pseudomonas fluorescens F113]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 424/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10   RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N++  I 
Sbjct: 190  VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             +E++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GHEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 415/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10  RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +  + D   E  +  +          +  +F  ++   +  RKA +K G N++  I 
Sbjct: 190 VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            +E++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GHEVDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|146309042|ref|YP_001189507.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina ymp]
 gi|145577243|gb|ABP86775.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas mendocina ymp]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/612 (50%), Positives = 422/612 (68%), Gaps = 22/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130  REVMSAIAHFPGTVEGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 1012 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            + ++  +A               +           E+  +FS ++   +K++KA +K G 
Sbjct: 183  VPVKEGAAAEESDDEEDEESGDDEEEEGDGGPDPEEAARRFSAVAEQQEKVQKALKKHGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S+   +    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243  GSKQATEELAALAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303  DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483  EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            P+R   L+ FL+
Sbjct: 603  PTRSEHLRSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/599 (50%), Positives = 413/599 (68%), Gaps = 22/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130 REVMSAIAHFPGTVEGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 222 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           + ++  +A               +           E+  +FS ++   +K++KA +K G 
Sbjct: 183 VPVKEGAAAEESDDEEDEESGDDEEEEGDGGPDPEEAARRFSAVAEQQEKVQKALKKHGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S+   +    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243 GSKQATEELAALAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303 DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483 EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|404398429|ref|ZP_10990013.1| RNA polymerase sigma factor RpoD [Pseudomonas fuscovaginae UPB0736]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 423/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL   ++++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDYILDEYNRVTSEGGRLSDVLSGYIDPDDGIALPAAEVPPPVDAKT 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              E     E   +D   E+  +   + ++   +F  ++   +  RKA +K G  +++ I 
Sbjct: 190  GKENATDDEDEESDSDDEEEVESGPDPIVAAQRFGAVADQLEIARKALKKHGRGNKATIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ + ++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLLLAELFMPIKLVPKQFEVLVERVRSALERLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NEI+ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEIDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 414/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL   ++++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDYILDEYNRVTSEGGRLSDVLSGYIDPDDGIALPAAEVPPPVDAKT 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
             E     E   +D   E+  +   + ++   +F  ++   +  RKA +K G  +++ I 
Sbjct: 190 GKENATDDEDEESDSDDEEEVESGPDPIVAAQRFGAVADQLEIARKALKKHGRGNKATIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ + ++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLLLAELFMPIKLVPKQFEVLVERVRSALERLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NEI+ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEIDESWTDALAKGKSKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|330505280|ref|YP_004382149.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
 gi|328919566|gb|AEB60397.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina NK-01]
          Length = 615

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/612 (50%), Positives = 423/612 (69%), Gaps = 22/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130  REVMSAIAHFPGTVDGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 1012 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            + ++  +A               +           E+  +F+ ++   +K++KA +K G 
Sbjct: 183  VPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARRFTAVAEQQEKVQKALKKHGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S+  I+    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243  GSKQAIEELATLAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303  DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483  EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            P+R   L+ FL+
Sbjct: 603  PTRSEHLRSFLD 614



 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/599 (50%), Positives = 414/599 (69%), Gaps = 22/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130 REVMSAIAHFPGTVDGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 222 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           + ++  +A               +           E+  +F+ ++   +K++KA +K G 
Sbjct: 183 VPVKEGAAAEESDDEEEDESGDDEEEEGDGGPDPEEAARRFTAVAEQQEKVQKALKKHGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S+  I+    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243 GSKQAIEELATLAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303 DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483 EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|339485320|ref|YP_004699848.1| RNA polymerase sigma factor RpoD [Pseudomonas putida S16]
 gi|431800439|ref|YP_007227342.1| RNA polymerase sigma factor RpoD [Pseudomonas putida HB3267]
 gi|338836163|gb|AEJ10968.1| RNA polymerase sigma factor RpoD [Pseudomonas putida S16]
 gi|430791204|gb|AGA71399.1| RNA polymerase sigma factor RpoD [Pseudomonas putida HB3267]
 gi|451775006|gb|AGF50254.1| RNA polymerase sigma-70 factor RpoD [Pseudomonas putida]
          Length = 616

 Score =  600 bits (1548), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/606 (51%), Positives = 421/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130  REVMGAIAHFPGTVDYILSEYDRVTSEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++   +      S +  E+ +       +  +F  ++       K  +K G   +  I
Sbjct: 190  AAKEESDDDEDESESGDDEEEAESGPDPEVARQRFGAVNDQLQATNKVLKKNGRTHQESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  DALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/593 (51%), Positives = 412/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130 REVMGAIAHFPGTVDYILSEYDRVTSEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++   +      S +  E+ +       +  +F  ++       K  +K G   +  I
Sbjct: 190 AAKEESDDDEDESESGDDEEEAESGPDPEVARQRFGAVNDQLQATNKVLKKNGRTHQESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 DALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|398967711|ref|ZP_10682061.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM30]
 gi|398144472|gb|EJM33304.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM30]
          Length = 615

 Score =  600 bits (1547), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/601 (52%), Positives = 424/601 (70%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKAAKAD 193

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  +S   +  RKA +K G ++++ I     
Sbjct: 194  DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRHNKAAIAELLA 253

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254  LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE K
Sbjct: 314  DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAK 373

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 554  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 613

Query: 1428 E 1428
            +
Sbjct: 614  D 614



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/588 (52%), Positives = 415/588 (70%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKAAKAD 193

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  +S   +  RKA +K G ++++ I     
Sbjct: 194 DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRHNKAAIAELLA 253

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254 LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKLI L+T+  L + +++DINR+M  GE K
Sbjct: 314 DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLIALETETGLTIAEIKDINRRMSIGEAK 373

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|344339320|ref|ZP_08770249.1| RNA polymerase, sigma 70 subunit, RpoD [Thiocapsa marina 5811]
 gi|343800624|gb|EGV18569.1| RNA polymerase, sigma 70 subunit, RpoD [Thiocapsa marina 5811]
          Length = 610

 Score =  600 bits (1547), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 310/597 (51%), Positives = 418/597 (70%), Gaps = 3/597 (0%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 894
            LI  GKE+GYLT+SE+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13   LIAKGKEQGYLTYSEVNDHLPPGIVETDQIEDIVRMINDMGIMVHETAPDVVDHTLSDSA 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73   VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELVIAKRIEDGLNQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNEEKI 1012
            + A+S  P ++ +++   D++ + E ++ +++ G  D +    +  +V+   K  +E   
Sbjct: 133  LSALSVYPRSVEKLIEIFDRVEREETRLTDVISGFNDGDDEPVATPQVVGSEKAKDETDS 192

Query: 1013 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 1072
              +    D +         ++  +   +  HF  +R A E+ G + E    A  ++S   
Sbjct: 193  ESDDDDDDAAVVDTGPDPEDAARRAQLLREHFAVLRSALEQYGRDDERSRAAMASVSEVF 252

Query: 1073 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 1132
            L  +  A   ++L + LR+ I ++   E+ I+ + V + GMPR  FI  FPENE N  W+
Sbjct: 253  LQFKLVAPIFQELAELLRHTIERIRGQERVIMSLCVEQAGMPRKVFIDTFPENETNPQWL 312

Query: 1133 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 1192
            + +      Y   L      I+  Q+KL  ++ + +L +++++D+NRKM  GE KAR+AK
Sbjct: 313  EQQLASGKPYAARLAEVAQDIRRAQRKLQEMEKENILTISEVKDVNRKMSIGEAKARRAK 372

Query: 1193 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252
            +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 373  KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 432

Query: 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 1312
            QAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +M+MPE+K+RK
Sbjct: 433  QAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAQRMDMPEDKVRK 492

Query: 1313 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 1372
            ++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT RE+
Sbjct: 493  VLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVDSATAEGLREATQNMLASLTSREA 552

Query: 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  KL+ FL+ 
Sbjct: 553  KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKLRSFLDA 609



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 306/591 (51%), Positives = 411/591 (69%), Gaps = 4/591 (0%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 104
           LI  GKE+GYLT+SE+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13  LIAKGKEQGYLTYSEVNDHLPPGIVETDQIEDIVRMINDMGIMVHETAPDVVDHTLSDSA 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73  VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELVIAKRIEDGLNQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNEEKI 222
           + A+S  P ++ +++   D++ + E ++ +++ G  D +    +  +V+   K  +E   
Sbjct: 133 LSALSVYPRSVEKLIEIFDRVEREETRLTDVISGFNDGDDEPVATPQVVGSEKAKDETDS 192

Query: 223 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 282
             +    D +         ++  +   +  HF  +R A E+ G + E    A  ++S   
Sbjct: 193 ESDDDDDDAAVVDTGPDPEDAARRAQLLREHFAVLRSALEQYGRDDERSRAAMASVSEVF 252

Query: 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 342
           L  +  A   ++L + LR+ I ++   E+ I+ + V + GMPR  FI  FPENE N  W+
Sbjct: 253 LQFKLVAPIFQELAELLRHTIERIRGQERVIMSLCVEQAGMPRKVFIDTFPENETNPQWL 312

Query: 343 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           + +      Y   L      I+  Q+KL  ++ + +L +++++D+NRKM  GE KAR+AK
Sbjct: 313 EQQLASGKPYAARLAEVAQDIRRAQRKLQEMEKENILTISEVKDVNRKMSIGEAKARRAK 372

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 373 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 432

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +M+MPE+K+RK
Sbjct: 433 QAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAQRMDMPEDKVRK 492

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           ++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT RE+
Sbjct: 493 VLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVDSATAEGLREATQNMLASLTSREA 552

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 553 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKL 603


>gi|395651014|ref|ZP_10438864.1| RNA polymerase sigma factor RpoD [Pseudomonas extremaustralis 14-3
            substr. 14-3b]
          Length = 616

 Score =  600 bits (1547), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 312/608 (51%), Positives = 421/608 (69%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----------FSSNNRV 1000
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +              + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +K + ++ ++     +   D      + +      +F  +S   +  RKA +K G +++ 
Sbjct: 190  VKADDDSEDDDAEASTDDEDEVESGPDPIIAAQ--RFGAVSDQMEITRKALKKHGRSNKL 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++
Sbjct: 248  AIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             FP NE++ +W D   K +  Y   + R  P I   Q KL  L+T+  L + +++DINR+
Sbjct: 308  QFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQHKLTALETETGLTIAEIKDINRR 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 488  ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R 
Sbjct: 548  RDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 607

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 608  EHLRSFLD 615



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/595 (51%), Positives = 412/595 (69%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----------FSSNNRV 210
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +              + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +K + ++ ++     +   D      + +      +F  +S   +  RKA +K G +++ 
Sbjct: 190 VKADDDSEDDDAEASTDDEDEVESGPDPIIAAQ--RFGAVSDQMEITRKALKKHGRSNKL 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++
Sbjct: 248 AIAELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRADFLR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            FP NE++ +W D   K +  Y   + R  P I   Q KL  L+T+  L + +++DINR+
Sbjct: 308 QFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQHKLTALETETGLTIAEIKDINRR 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 488 ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|399000528|ref|ZP_10703254.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM18]
 gi|398129755|gb|EJM19111.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM18]
          Length = 615

 Score =  600 bits (1547), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 425/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  +  + D   E  +  +          +  +F  ++   +  RKA +K G  +++ I 
Sbjct: 190  VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRYNKAAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 416/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +        +     + + 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKA 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  +  + D   E  +  +          +  +F  ++   +  RKA +K G  +++ I 
Sbjct: 190 VKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRYNKAAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|398997186|ref|ZP_10700016.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM21]
 gi|398124679|gb|EJM14185.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM21]
          Length = 615

 Score =  600 bits (1547), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 424/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
                    +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190  APAADDTDDDDAEATDDEEEAESGPDPIIAAQRFGAVSDQMEITRKALKKHGRGNKLAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W +   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M  
Sbjct: 310  GNEVDESWTEALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/592 (52%), Positives = 415/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDPKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
                   +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190 APAADDTDDDDAEATDDEEEAESGPDPIIAAQRFGAVSDQMEITRKALKKHGRGNKLAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W +   K +  Y   + R  P I   QQKL  LQT+  L + +++DINR+M  
Sbjct: 310 GNEVDESWTEALAKGKSKYAEAIGRLQPDIIRCQQKLTALQTETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|402700981|ref|ZP_10848960.1| RNA polymerase sigma factor RpoD [Pseudomonas fragi A22]
          Length = 615

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 419/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKV 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              E     +        E+  +   + +I   +F  +S   +  RKA +K G  S+  I 
Sbjct: 190  KAEGDDEEDEKEESTEEEEEVESGPDPIIAAQRFGAVSDQMEIARKALKKHGRGSKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F+++FP
Sbjct: 250  ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/592 (52%), Positives = 410/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDPKV 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
             E     +        E+  +   + +I   +F  +S   +  RKA +K G  S+  I 
Sbjct: 190 KAEGDDEEDEKEESTEEEEEVESGPDPIIAAQRFGAVSDQMEIARKALKKHGRGSKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F+++FP
Sbjct: 250 ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRLFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLSALEAETGLKIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|395446767|ref|YP_006387020.1| RNA polymerase sigma factor RpoD [Pseudomonas putida ND6]
 gi|388560764|gb|AFK69905.1| RNA polymerase sigma factor RpoD [Pseudomonas putida ND6]
          Length = 616

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/606 (51%), Positives = 419/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 1010 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
                      + S    ++ + ES         +F  +S       K  +K G N +  I
Sbjct: 190  AAKEESDDDEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRNHKESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+ +  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKNAAIVACQQKLIDLEIETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/593 (51%), Positives = 410/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 220 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 272
                     + S    ++ + ES         +F  +S       K  +K G N +  I
Sbjct: 190 AAKEESDDDEEESESGDDEEEAESGPDPVVAAQRFGAVSDQLQATSKVLKKNGRNHKESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 EALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+ +  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKNAAIVACQQKLIDLEIETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|71891846|ref|YP_277575.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia pennsylvanicus
            str. BPEN]
 gi|71795952|gb|AAZ40703.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia pennsylvanicus
            str. BPEN]
          Length = 611

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 318/611 (52%), Positives = 427/611 (69%), Gaps = 14/611 (2%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT- 886
            N + + K+L+ LGKE+GYLTFSE+ND LPEDI+D   IE+II+    M I V E   ++ 
Sbjct: 4    NPQSQLKLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVMEEAPNSD 63

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            E L++ +  S +D E+ATEAA   L+ VDS+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 64   EFLLIEHTHSTNDEEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDI 123

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE+G+  +  ++S  P  I  +L    ++   E ++ +++ G +D + + N   I  
Sbjct: 124  AKRIEDGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLITGFVDPDINENIS-IHT 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            N N+   ++  ES S D   E  ++   +   + +KF+ +   +D  RK  +   YN  +
Sbjct: 183  NINHITAEVTTESISDDDEEENNDENNIDPEIAYVKFTALRNQYDITRKTIK---YNGRN 239

Query: 1061 YIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            +IK+   I   S      R   K  + L + +R+ + +V + E+ I+++ V    MP+ +
Sbjct: 240  HIKSSKEILKLSEIFKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVEISKMPKKN 299

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  N+ N  W +    +   ++  L +    ++    KL  ++ +  L +  ++DI
Sbjct: 300  FIALFSGNQTNKTWFNTALSMHTSWSEKLYKVDEDVQNSLSKLHQIEKETGLTIEQVKDI 359

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 420  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEIGHEPTPE 479

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M M E+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED N   P D+A + ++R
Sbjct: 480  ELAERMLMSEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTNHDLPLDSATSDNLR 539

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   DIL+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 540  TATHDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 599

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 600  SRSEILRSFLD 610



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 418/598 (69%), Gaps = 14/598 (2%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT- 96
           N + + K+L+ LGKE+GYLTFSE+ND LPEDI+D   IE+II+    M I V E   ++ 
Sbjct: 4   NPQSQLKLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVMEEAPNSD 63

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           E L++ +  S +D E+ATEAA   L+ VDS+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 64  EFLLIEHTHSTNDEEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDI 123

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE+G+  +  ++S  P  I  +L    ++   E ++ +++ G +D + + N   I  
Sbjct: 124 AKRIEDGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLITGFVDPDINENIS-IHT 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSES 270
           N N+   ++  ES S D   E  ++   +   + +KF+ +   +D  RK  +   YN  +
Sbjct: 183 NINHITAEVTTESISDDDEEENNDENNIDPEIAYVKFTALRNQYDITRKTIK---YNGRN 239

Query: 271 YIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           +IK+   I   S      R   K  + L + +R+ + +V + E+ I+++ V    MP+ +
Sbjct: 240 HIKSSKEILKLSEIFKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVEISKMPKKN 299

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  N+ N  W +    +   ++  L +    ++    KL  ++ +  L +  ++DI
Sbjct: 300 FIALFSGNQTNKTWFNTALSMHTSWSEKLYKVDEDVQNSLSKLHQIEKETGLTIEQVKDI 359

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 420 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEIGHEPTPE 479

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M M E+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED N   P D+A + ++R
Sbjct: 480 ELAERMLMSEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTNHDLPLDSATSDNLR 539

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   DIL+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 TATHDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|398890175|ref|ZP_10643862.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM55]
 gi|398188478|gb|EJM75780.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM55]
          Length = 615

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/605 (51%), Positives = 427/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKT 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +        E+  +   + +I   +F  ++   +  RKA +K G ++++ + 
Sbjct: 190  VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAVA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKGKYADAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 418/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELITLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMSAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKT 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +        E+  +   + +I   +F  ++   +  RKA +K G ++++ + 
Sbjct: 190 VKADDDSDDEDGEASDDEEEAESGPDPIIAAQRFGAVADQMEITRKALKKHGRHNKAAVA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALADLFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKGKYADAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|440509639|ref|YP_007347075.1| RNA polymerase sigma factor [Candidatus Blochmannia chromaiodes str.
            640]
 gi|440453852|gb|AGC03344.1| RNA polymerase sigma factor [Candidatus Blochmannia chromaiodes str.
            640]
          Length = 611

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 318/611 (52%), Positives = 428/611 (70%), Gaps = 14/611 (2%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT- 886
            N + + K+L+ LGKE+GYLTFSE+ND LPEDI+D   IE+II+    M I V E   ++ 
Sbjct: 4    NPQSQLKLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVIEEAPNSD 63

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            E L++ N  S +D E+ATEAA   L+ VDS+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 64   EFLLIENTHSTNDEEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDI 123

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE+G+  +  ++S  P  I  +L    ++   E ++ +++ G +D + + N   I  
Sbjct: 124  AKRIEDGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLITGFVDPDINENIS-IHT 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            N N+   ++  ES S D   E  ++   +   + +KF+ +   +D  RK  +   YN  +
Sbjct: 183  NINHITAEVTTESISDDDEEENNDENNIDPEIAYVKFTALRNQYDITRKTIK---YNGRN 239

Query: 1061 YIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            +IK+   I   S      R   K  + L + +R+ + +V + E+ I+++ V    MP+ +
Sbjct: 240  HIKSSKEILKLSEIFKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVEISKMPKKN 299

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  N+ N  W +    ++  ++  L +    ++    KL  ++ +  L +  ++DI
Sbjct: 300  FIALFSGNQTNKTWFNTALSMRTSWSEKLYKVDEDVQNSLSKLHQIEKETGLTIEQVKDI 359

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 420  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEIGHEPTPE 479

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M M E+KIRK++KI+KEP+SME+PVGDDEDSHLGDFIED N   P D+A + ++R
Sbjct: 480  ELAERMLMSEDKIRKVLKISKEPISMETPVGDDEDSHLGDFIEDTNHDLPLDSATSDNLR 539

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   DIL+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 540  TATHDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 599

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 600  SRSEILRSFLD 610



 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 311/598 (52%), Positives = 419/598 (70%), Gaps = 14/598 (2%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT- 96
           N + + K+L+ LGKE+GYLTFSE+ND LPEDI+D   IE+II+    M I V E   ++ 
Sbjct: 4   NPQSQLKLLVTLGKEQGYLTFSEVNDHLPEDIVDPGQIENIIQMMNDMGIQVIEEAPNSD 63

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           E L++ N  S +D E+ATEAA   L+ VDS+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 64  EFLLIENTHSTNDEEDATEAAVQALTNVDSELGRTTDPVRMYMREMGTVELLTREGEIDI 123

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE+G+  +  ++S  P  I  +L    ++   E ++ +++ G +D + + N   I  
Sbjct: 124 AKRIEDGINQVQCSVSEYPEAITYLLEQYKRVETGETRLSDLITGFVDPDINENIS-IHT 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSES 270
           N N+   ++  ES S D   E  ++   +   + +KF+ +   +D  RK  +   YN  +
Sbjct: 183 NINHITAEVTTESISDDDEEENNDENNIDPEIAYVKFTALRNQYDITRKTIK---YNGRN 239

Query: 271 YIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           +IK+   I   S      R   K  + L + +R+ + +V + E+ I+++ V    MP+ +
Sbjct: 240 HIKSSKEILKLSEIFKQFRLVPKQFDYLVNNMRSMMERVRKQERLIMKLCVEISKMPKKN 299

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  N+ N  W +    ++  ++  L +    ++    KL  ++ +  L +  ++DI
Sbjct: 300 FIALFSGNQTNKTWFNTALSMRTSWSEKLYKVDEDVQNSLSKLHQIEKETGLTIEQVKDI 359

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 420 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEIGHEPTPE 479

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M M E+KIRK++KI+KEP+SME+PVGDDEDSHLGDFIED N   P D+A + ++R
Sbjct: 480 ELAERMLMSEDKIRKVLKISKEPISMETPVGDDEDSHLGDFIEDTNHDLPLDSATSDNLR 539

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   DIL+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 TATHDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|70732951|ref|YP_262722.1| RNA polymerase sigma factor RpoD [Pseudomonas protegens Pf-5]
 gi|1710687|sp|P52326.1|RPOD_PSEFL RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|929808|emb|CAA59134.1| sigma 70 [Pseudomonas protegens]
 gi|68347250|gb|AAY94856.1| RNA polymerase sigma factor RpoD [Pseudomonas protegens Pf-5]
          Length = 615

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 421/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPVDTKT 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  ++   +  RKA +K G  ++  I 
Sbjct: 190  AKADDDSEDEEAEATEDEEEAESGPDPVIAAQRFGAVADQMEVTRKALKKHGRENKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  EMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEVDESWTDALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/592 (51%), Positives = 412/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPVDTKT 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  ++   +  RKA +K G  ++  I 
Sbjct: 190 AKADDDSEDEEAEATEDEEEAESGPDPVIAAQRFGAVADQMEVTRKALKKHGRENKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 EMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEVDESWTDALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|409418289|ref|ZP_11258288.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. HYS]
          Length = 615

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 421/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +   +    V         
Sbjct: 130  REVMGAIAHFPGTVEHILSEYDRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPIDPKAP 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
             K   +    +   ++ E+          +  +F  +    +   K  +K G + +  +K
Sbjct: 190  AKAEADDEDEEKEGDEEEEETESGPDPEVARQRFGAVQDQLNATLKVLKKNGRSHKDSLK 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A  +++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F+++FP
Sbjct: 250  AMLDLAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NEI+  W  +  K    +   L     +I   QQKLI+L+++  L + +++DINR+M  
Sbjct: 310  SNEIDQTWASDLAKRSTKWATALGEKSDAIVACQQKLIDLESETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/592 (51%), Positives = 412/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +   +    V         
Sbjct: 130 REVMGAIAHFPGTVEHILSEYDRVTTEGGRLSDVLSGYIDPDDGIAPPAEVPPPIDPKAP 189

Query: 220 EKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
            K   +    +   ++ E+          +  +F  +    +   K  +K G + +  +K
Sbjct: 190 AKAEADDEDEEKEGDEEEEETESGPDPEVARQRFGAVQDQLNATLKVLKKNGRSHKDSLK 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A  +++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F+++FP
Sbjct: 250 AMLDLAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NEI+  W  +  K    +   L     +I   QQKLI+L+++  L + +++DINR+M  
Sbjct: 310 SNEIDQTWASDLAKRSTKWATALGEKSDAIVACQQKLIDLESETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|3646419|emb|CAA07705.1| sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score =  600 bits (1546), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/618 (50%), Positives = 422/618 (68%), Gaps = 33/618 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V +D GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVKTDIGRTTDPVRMYMREMGTVELLTREGEIGIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL   ++++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDRILSEYNRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 994  ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                  +      +  ++E+++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190  AKADDDSEDDDAESSGDDEDEV--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238  LKKHGRTNKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L 
Sbjct: 298  ARMPRADFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLT 357

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358  IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478  GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538  ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHP+R   L+ FL+
Sbjct: 598  LRKLRHPTRSEHLRSFLD 615



 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/605 (51%), Positives = 413/605 (68%), Gaps = 33/605 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELIVLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEAAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V +D GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVKTDIGRTTDPVRMYMREMGTVELLTREGEIGIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL   ++++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDRILSEYNRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 204 ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
                 +      +  ++E+++  ES    +   Q          +F  +S   +  RKA
Sbjct: 190 AKADDDSEDDDAESSGDDEDEV--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +K G  ++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238 LKKHGRTNKQAIAELIALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L 
Sbjct: 298 ARMPRADFLRQFPGNEVDESWTDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLT 357

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358 IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478 GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538 ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 621 LRKLR 625
           LRKLR
Sbjct: 598 LRKLR 602


>gi|77461370|ref|YP_350877.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf0-1]
 gi|77385373|gb|ABA76886.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas fluorescens
            Pf0-1]
          Length = 615

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 313/601 (52%), Positives = 422/601 (70%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-----GNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +        +       K    +
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPIDAKAAKAD 193

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ I     
Sbjct: 194  DDSEDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRHNKAAIAELLA 253

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254  LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314  DESWSDALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 554  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 613

Query: 1428 E 1428
            +
Sbjct: 614  D 614



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/588 (52%), Positives = 413/588 (70%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-----GNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +        +       K    +
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGITPPAAEVPPPIDAKAAKAD 193

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ I     
Sbjct: 194 DDSEDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRHNKAAIAELLA 253

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254 LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314 DESWSDALAKGKSKYAEAIARVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|423693922|ref|ZP_17668442.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens SS101]
 gi|388002264|gb|EIK63593.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens SS101]
          Length = 615

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/605 (52%), Positives = 423/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190  AKADDDTDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/592 (52%), Positives = 414/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190 AKADDDTDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|423093350|ref|ZP_17081146.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Q2-87]
 gi|397882398|gb|EJK98885.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Q2-87]
          Length = 615

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 424/605 (70%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10   RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  ++   +  RKA +K G N++  I 
Sbjct: 190  AKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEVDESWTDALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 415/592 (70%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + LML
Sbjct: 10  RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDKDALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  ++   +  RKA +K G N++  I 
Sbjct: 190 AKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRNNKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEVDESWTDALAKGKSKYAEAIARLQPDIVRCQQKLSALEAETGLSIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|359780768|ref|ZP_09283993.1| RNA polymerase sigma factor RpoD [Pseudomonas psychrotolerans L19]
 gi|359370828|gb|EHK71394.1| RNA polymerase sigma factor RpoD [Pseudomonas psychrotolerans L19]
          Length = 617

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 314/615 (51%), Positives = 419/615 (68%), Gaps = 26/615 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AETDTDEAAAEEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +         G+  N  ++
Sbjct: 130  REVMGAIAQFPGTVDYILSEYTRVTTEGGRLSDVLAGYIDPD--------DGSLPNESDE 181

Query: 1012 ILIESSSADLSTEQLEKLKY------------------ESLIKFSNISFHFDKMRKAFEK 1053
            + + + +AD      EK +                   E+ ++F  ++   +K +K  +K
Sbjct: 182  LPVPNKAADAKAVDDEKDEEEESDDDAEEEGDGGPDPEEARLRFGAVAEQLEKTQKVLKK 241

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G + +  ++    ++     I+   K  E L   +R  + +V  +E+ I+++ V    M
Sbjct: 242  HGRDDDRAVEEFVALALLFSPIKLVPKQYEALVTRVRESLERVRGLERAIMQLAVRDARM 301

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            PR  F++ FP NE N  W     K +  Y   L R    I+  Q +L  L+ D  L ++ 
Sbjct: 302  PRADFLRHFPGNETNTEWTAGLLKGKPKYAEGLERFQADIQAKQAQLAELERDYELKVSQ 361

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DINR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 362  IKDINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 421

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 422  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 481

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A +
Sbjct: 482  PTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATS 541

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 542  ESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 601

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 602  LRHPSRSEHLRSFLD 616



 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/602 (50%), Positives = 410/602 (68%), Gaps = 26/602 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AETDTDEAAAEEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +         G+  N  ++
Sbjct: 130 REVMGAIAQFPGTVDYILSEYTRVTTEGGRLSDVLAGYIDPD--------DGSLPNESDE 181

Query: 222 ILIESSSADLSTEQLEKLKY------------------ESLIKFSNISFHFDKMRKAFEK 263
           + + + +AD      EK +                   E+ ++F  ++   +K +K  +K
Sbjct: 182 LPVPNKAADAKAVDDEKDEEEESDDDAEEEGDGGPDPEEARLRFGAVAEQLEKTQKVLKK 241

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G + +  ++    ++     I+   K  E L   +R  + +V  +E+ I+++ V    M
Sbjct: 242 HGRDDDRAVEEFVALALLFSPIKLVPKQYEALVTRVRESLERVRGLERAIMQLAVRDARM 301

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           PR  F++ FP NE N  W     K +  Y   L R    I+  Q +L  L+ D  L ++ 
Sbjct: 302 PRADFLRHFPGNETNTEWTAGLLKGKPKYAEGLERFQADIQAKQAQLAELERDYELKVSQ 361

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DINR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 362 IKDINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 421

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 422 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 481

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A +
Sbjct: 482 PTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATS 541

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 542 ESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 601

Query: 624 LR 625
           LR
Sbjct: 602 LR 603


>gi|350560602|ref|ZP_08929442.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio
            thiocyanoxidans ARh 4]
 gi|349782870|gb|EGZ37153.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio
            thiocyanoxidans ARh 4]
          Length = 620

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 309/617 (50%), Positives = 422/617 (68%), Gaps = 17/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GKE+GYLT++E+ND LP+ IID + IE II     M I+V E   D 
Sbjct: 4    EEQQSQLKELIARGKEQGYLTYTEVNDHLPDSIIDSDQIEDIIAMINDMGIAVHEQAPDA 63

Query: 887  ETLMLSNITSDDDVEEATEAALSTVD-SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            +TL+LS+ +   D +     A      SDFGRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 64   DTLLLSDGSVSSDDDAEDAVAALAAVDSDFGRTTDPVRMYMREMGTVELLTREGEIRIAK 123

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEGL  ++ A++  P+ I ++L    ++ +N  ++ ++V   I+        V +G  
Sbjct: 124  RIEEGLMQVLFALAHHPSAISQLLEQYQRLVENNTRLTDLVVSFINPEAGDGEAVARGLA 183

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------------ESLIKFSNISFHFDKMRKAF 1051
                      S+SAD S E  +                  E+ ++F+ ++   +  ++A 
Sbjct: 184  EPGAATEAPPSASADTSDEDSDDTDDDSDEEVEDTGPDPEEARVRFARLAELHNAAQEAC 243

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            +++ Y++  Y +A    +   +  +   + +++L   L   I ++ + E+QI+++VV + 
Sbjct: 244  QRKDYDA--YTRAREETARYFMEFKLVPRVVDELTSNLHATIGKIRRYERQIMQLVVAQA 301

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MPR  F+  FP+NE NL+W+    K +  Y   L      +  LQ+KL+ ++    L +
Sbjct: 302  RMPRKVFLDSFPKNETNLDWIAQAQKAKGKYTEQLAEVADEVVRLQKKLLEIEKRANLSI 361

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
             +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 362  AEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 421

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G
Sbjct: 422  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMG 481

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             E  P  +A +MEMPE+KIRK+MKI+KEP+SME+P+GDDEDSHLGDFIEDE ++ P ++A
Sbjct: 482  REATPEELAERMEMPEDKIRKVMKISKEPISMETPIGDDEDSHLGDFIEDEKVMTPVESA 541

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
              A +    ++IL +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 542  ARAKLSEATREILATLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 601

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHP+R   L+ +++
Sbjct: 602  RKLRHPTRAELLRSYMD 618



 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 413/604 (68%), Gaps = 17/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GKE+GYLT++E+ND LP+ IID + IE II     M I+V E   D 
Sbjct: 4   EEQQSQLKELIARGKEQGYLTYTEVNDHLPDSIIDSDQIEDIIAMINDMGIAVHEQAPDA 63

Query: 97  ETLMLSNITSDDDVEEATEAALSTVD-SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           +TL+LS+ +   D +     A      SDFGRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 64  DTLLLSDGSVSSDDDAEDAVAALAAVDSDFGRTTDPVRMYMREMGTVELLTREGEIRIAK 123

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEGL  ++ A++  P+ I ++L    ++ +N  ++ ++V   I+        V +G  
Sbjct: 124 RIEEGLMQVLFALAHHPSAISQLLEQYQRLVENNTRLTDLVVSFINPEAGDGEAVARGLA 183

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------------ESLIKFSNISFHFDKMRKAF 261
                     S+SAD S E  +                  E+ ++F+ ++   +  ++A 
Sbjct: 184 EPGAATEAPPSASADTSDEDSDDTDDDSDEEVEDTGPDPEEARVRFARLAELHNAAQEAC 243

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           +++ Y++  Y +A    +   +  +   + +++L   L   I ++ + E+QI+++VV + 
Sbjct: 244 QRKDYDA--YTRAREETARYFMEFKLVPRVVDELTSNLHATIGKIRRYERQIMQLVVAQA 301

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MPR  F+  FP+NE NL+W+    K +  Y   L      +  LQ+KL+ ++    L +
Sbjct: 302 RMPRKVFLDSFPKNETNLDWIAQAQKAKGKYTEQLAEVADEVVRLQKKLLEIEKRANLSI 361

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 362 AEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 421

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G
Sbjct: 422 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMG 481

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            E  P  +A +MEMPE+KIRK+MKI+KEP+SME+P+GDDEDSHLGDFIEDE ++ P ++A
Sbjct: 482 REATPEELAERMEMPEDKIRKVMKISKEPISMETPIGDDEDSHLGDFIEDEKVMTPVESA 541

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
             A +    ++IL +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 542 ARAKLSEATREILATLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 601

Query: 622 RKLR 625
           RKLR
Sbjct: 602 RKLR 605


>gi|89094383|ref|ZP_01167323.1| RNA polymerase sigma factor [Neptuniibacter caesariensis]
 gi|89081275|gb|EAR60507.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 616

 Score =  599 bits (1545), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 317/604 (52%), Positives = 425/604 (70%), Gaps = 7/604 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT+SE+ND LP+DI D + +E II+    M ISVSE   D ETL++
Sbjct: 11   RLKELIARGKEQGYLTYSEVNDHLPQDIADPDQVEDIIRMINDMGISVSEEAPDAETLLM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   S ++ +E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRIEEGL
Sbjct: 71   TEGDSAEEADEEAVAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGL 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--NRVIKGNKNNNE 1009
            ++++ A++  P T+  IL A     + E ++ +I  G ID +        VI G++ +  
Sbjct: 131  REVMSAVACFPGTVESILEAYKLTLEEEGRLSDIFSGYIDADDDEEIPAAVIPGSEEDLS 190

Query: 1010 EKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            ++   E   +D   ++ ++ +      E+  +F  +S ++D +  A +K G +S+ +  A
Sbjct: 191  DEDDDEDEDSDDDDDEEDEKEKGPDPEEAARRFGLLSDNYDALLIALDKHGRDSKEFGAA 250

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
               +S     I+   +  E L + +R+ I  +   E+ I+ I   +  MPR  FIK FP 
Sbjct: 251  QVELSESFAPIKLAPRYYEALVNQVRSTIENIRNQERTIMRICTQRAKMPRKTFIKEFPG 310

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE+N +W +   +    Y+  +  N+  +K  Q+KLI  + +  + L +++++NR+M  G
Sbjct: 311  NEVNADWFNQVIESGESYSRAIKTNLIELKRAQKKLIQAEIETGISLAEIKEVNRRMSIG 370

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 371  EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +ME
Sbjct: 431  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERME 490

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A    +R   +++L
Sbjct: 491  MPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSPVDSATGEGLREATREVL 550

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+
Sbjct: 551  AGLTVRESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLR 610

Query: 1425 IFLE 1428
             FL+
Sbjct: 611  GFLD 614



 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/591 (52%), Positives = 416/591 (70%), Gaps = 7/591 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT+SE+ND LP+DI D + +E II+    M ISVSE   D ETL++
Sbjct: 11  RLKELIARGKEQGYLTYSEVNDHLPQDIADPDQVEDIIRMINDMGISVSEEAPDAETLLM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   S ++ +E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRIEEGL
Sbjct: 71  TEGDSAEEADEEAVAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGL 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--NRVIKGNKNNNE 219
           ++++ A++  P T+  IL A     + E ++ +I  G ID +        VI G++ +  
Sbjct: 131 REVMSAVACFPGTVESILEAYKLTLEEEGRLSDIFSGYIDADDDEEIPAAVIPGSEEDLS 190

Query: 220 EKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           ++   E   +D   ++ ++ +      E+  +F  +S ++D +  A +K G +S+ +  A
Sbjct: 191 DEDDDEDEDSDDDDDEEDEKEKGPDPEEAARRFGLLSDNYDALLIALDKHGRDSKEFGAA 250

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
              +S     I+   +  E L + +R+ I  +   E+ I+ I   +  MPR  FIK FP 
Sbjct: 251 QVELSESFAPIKLAPRYYEALVNQVRSTIENIRNQERTIMRICTQRAKMPRKTFIKEFPG 310

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NE+N +W +   +    Y+  +  N+  +K  Q+KLI  + +  + L +++++NR+M  G
Sbjct: 311 NEVNADWFNQVIESGESYSRAIKTNLIELKRAQKKLIQAEIETGISLAEIKEVNRRMSIG 370

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 371 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +ME
Sbjct: 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERME 490

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A    +R   +++L
Sbjct: 491 MPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSPVDSATGEGLREATREVL 550

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 AGLTVRESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|253991033|ref|YP_003042389.1| rna polymerase, sigma(70) factor; regulation of proteins induced a
            high temperatures (rna polymerase sigma 70 factor rpod)
            [Photorhabdus asymbiotica]
 gi|253782483|emb|CAQ85647.1| rna polymerase, sigma(70) factor; regulation of proteins induced a
            high temperatures (rna polymerase sigma 70 factor rpod)
            [Photorhabdus asymbiotica]
          Length = 651

 Score =  599 bits (1544), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/664 (48%), Positives = 438/664 (65%), Gaps = 46/664 (6%)

Query: 784  IIKFLFLPDKYDPDSYIRKFGYKIFSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKER 843
            I+  L LP   +P++   K GY++                   +N + + K+L+  GKE+
Sbjct: 14   IVGRLVLPTDTNPNTL--KCGYRLME-----------------QNPQSQLKLLVTRGKEQ 54

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEA 903
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + LML+  T+D D E+A
Sbjct: 55   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAETTNDTD-EDA 113

Query: 904  TEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISS 960
             EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++ 
Sbjct: 114  VEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAE 173

Query: 961  CPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVIKGNKNNNEEKILIESS 1017
             P  I  +L   D++   E ++ +++ G +D N   +        G++   EE    +  
Sbjct: 174  YPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATHVGSELPQEELDDDDDE 233

Query: 1018 SADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 1071
              + + +  +     S+       KF  +   ++  R+  +K G       + H N + E
Sbjct: 234  DDEDNDDDSDGDDDNSIDPELARQKFQELHEQYEITRQEIKKNG-------RDHANTTAE 286

Query: 1072 MLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
            +L +       R   K  + L + +R+ +++V   E+QI+++ V +C MP+ +FI +F  
Sbjct: 287  ILKLSEIFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPKKNFITLFSG 346

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE +  W      +   ++  L      I+   Q+L  ++ +  L +  ++DINR+M  G
Sbjct: 347  NETSDIWFTAAKAMNKPWSEKLLEVEEEIQRSLQRLRQIEEETGLTIEQVKDINRRMSIG 406

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 407  EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 466

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M 
Sbjct: 467  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 526

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS   D+L
Sbjct: 527  MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATHDVL 586

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+
Sbjct: 587  AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 646

Query: 1425 IFLE 1428
             FL+
Sbjct: 647  SFLD 650



 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/608 (50%), Positives = 415/608 (68%), Gaps = 27/608 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 38  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 97

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + LML+  T+D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 98  DDLMLAETTNDTD-EDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 156

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRV 210
           AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      
Sbjct: 157 AKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTAT 216

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKE 264
             G++   EE    +    + + +  +     S+       KF  +   ++  R+  +K 
Sbjct: 217 HVGSELPQEELDDDDDEDDEDNDDDSDGDDDNSIDPELARQKFQELHEQYEITRQEIKKN 276

Query: 265 GYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           G       + H N + E+L +       R   K  + L + +R+ +++V   E+QI+++ 
Sbjct: 277 G-------RDHANTTAEILKLSEIFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMC 329

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V +C MP+ +FI +F  NE +  W      +   ++  L      I+   Q+L  ++ + 
Sbjct: 330 VEQCKMPKKNFITLFSGNETSDIWFTAAKAMNKPWSEKLLEVEEEIQRSLQRLRQIEEET 389

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 390 GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 449

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 450 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 509

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 510 QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 569

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 570 LDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 629

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 630 AKALRKLR 637


>gi|397664801|ref|YP_006506339.1| RNA polymerase, sigma 70 (sigma D) factor [Legionella pneumophila
            subsp. pneumophila]
 gi|395128212|emb|CCD06417.1| RNA polymerase, sigma 70 (sigma D) factor [Legionella pneumophila
            subsp. pneumophila]
          Length = 621

 Score =  599 bits (1544), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/607 (53%), Positives = 422/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314  TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 552  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 611

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 612  LRSFLEG 618



 Score =  578 bits (1489), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/593 (52%), Positives = 411/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314 TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|54295203|ref|YP_127618.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
            str. Lens]
 gi|53755035|emb|CAH16523.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
            str. Lens]
          Length = 621

 Score =  599 bits (1544), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/607 (53%), Positives = 421/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314  TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 552  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 611

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 612  LRSFLEG 618



 Score =  578 bits (1489), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/593 (52%), Positives = 410/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314 TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|390952273|ref|YP_006416032.1| RNA polymerase sigma-70 subunit RpoD [Thiocystis violascens DSM 198]
 gi|390428842|gb|AFL75907.1| RNA polymerase, sigma 70 subunit, RpoD [Thiocystis violascens DSM
            198]
          Length = 616

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 418/605 (69%), Gaps = 15/605 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 894
            LI  GKE+GYLT+SE+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13   LIAKGKEQGYLTYSEVNDHLPPGIVETDQIEDIVRMINDMGIMVQEVAPDVVDHTLSDSA 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73   VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELIIAKRIEDGLNQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            + A+S  P T+ +++   D++ + E ++ + + G  D        V+  +    E +I  
Sbjct: 133  LAALSVYPRTVEKLIEIFDRVEREETRLTDAISGFNDGEEEVALHVVHAHV---EPEIQA 189

Query: 1015 ESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +    DL  +  +     +++           + + +   FD +R A E+ G + E    
Sbjct: 190  DKPDTDLEADVDDDDASTAVVYTGPDPEDAAQRAALLRERFDVLRAALEQYGRDDERSRA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   +S   L  +  A   ++L + LR  I ++   E+ ++ + + + GMPR  FI  FP
Sbjct: 250  AMAEVSEVFLQFKLVAPVFQELTEILRTTIARIRAQERLLMALCIEQAGMPRKLFIDSFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
            +NE N +W++ +      Y   L      I+  Q+KL  L+ + +L + +++++NRKM  
Sbjct: 310  KNEANPDWLEQQLASGQPYAPRLAELAQDIRRAQRKLQELERENILTIGEIKEVNRKMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +AI+M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAIRM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++
Sbjct: 490  EMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVDSATAEGLREATQNM 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  KL
Sbjct: 550  LASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/592 (51%), Positives = 408/592 (68%), Gaps = 15/592 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 104
           LI  GKE+GYLT+SE+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13  LIAKGKEQGYLTYSEVNDHLPPGIVETDQIEDIVRMINDMGIMVQEVAPDVVDHTLSDSA 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73  VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELIIAKRIEDGLNQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           + A+S  P T+ +++   D++ + E ++ + + G  D        V+  +    E +I  
Sbjct: 133 LAALSVYPRTVEKLIEIFDRVEREETRLTDAISGFNDGEEEVALHVVHAHV---EPEIQA 189

Query: 225 ESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +    DL  +  +     +++           + + +   FD +R A E+ G + E    
Sbjct: 190 DKPDTDLEADVDDDDASTAVVYTGPDPEDAAQRAALLRERFDVLRAALEQYGRDDERSRA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   +S   L  +  A   ++L + LR  I ++   E+ ++ + + + GMPR  FI  FP
Sbjct: 250 AMAEVSEVFLQFKLVAPVFQELTEILRTTIARIRAQERLLMALCIEQAGMPRKLFIDSFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
           +NE N +W++ +      Y   L      I+  Q+KL  L+ + +L + +++++NRKM  
Sbjct: 310 KNEANPDWLEQQLASGQPYAPRLAELAQDIRRAQRKLQELERENILTIGEIKEVNRKMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +AI+M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELAIRM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++
Sbjct: 490 EMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVDSATAEGLREATQNM 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|54298252|ref|YP_124621.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
            str. Paris]
 gi|397668024|ref|YP_006509561.1| RNA polymerase, sigma 70 (sigma D) factor [Legionella pneumophila
            subsp. pneumophila]
 gi|53752037|emb|CAH13463.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
            str. Paris]
 gi|395131435|emb|CCD09703.1| RNA polymerase, sigma 70 (sigma D) factor [Legionella pneumophila
            subsp. pneumophila]
          Length = 621

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/607 (53%), Positives = 422/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314  TDLSWL--ETIISKHAKKLDLDRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 552  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 611

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 612  LRSFLEG 618



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/593 (52%), Positives = 411/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314 TDLSWL--ETIISKHAKKLDLDRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|52842571|ref|YP_096370.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila subsp.
            pneumophila str. Philadelphia 1]
 gi|378778259|ref|YP_005186698.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila subsp.
            pneumophila ATCC 43290]
 gi|52629682|gb|AAU28423.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila subsp.
            pneumophila str. Philadelphia 1]
 gi|364509075|gb|AEW52599.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila subsp.
            pneumophila ATCC 43290]
          Length = 623

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/607 (53%), Positives = 421/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 18   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 76

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 77   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 135

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 136  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 195

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 196  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 255

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 256  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 315

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 316  TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 373

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 374  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 434  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 493

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 494  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 553

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 554  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 613

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 614  LRSFLEG 620



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/593 (52%), Positives = 410/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 18  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 76

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 77  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 135

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 136 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 195

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 196 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 255

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 256 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 315

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 316 TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 373

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 374 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 434 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 493

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 494 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 553

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|307611207|emb|CBX00855.1| RNA polymerase sigma factor rpoD [Legionella pneumophila 130b]
          Length = 619

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 322/607 (53%), Positives = 421/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 14   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 132  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 191

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 192  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 251

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 312  TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 490  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 550  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 609

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 610  LRSFLEG 616



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/593 (52%), Positives = 410/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 14  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 132 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 191

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 192 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 251

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 312 TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 490 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|421505678|ref|ZP_15952613.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina DLHK]
 gi|400343375|gb|EJO91750.1| RNA polymerase sigma factor RpoD [Pseudomonas mendocina DLHK]
          Length = 615

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 421/612 (68%), Gaps = 22/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPE I D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEGISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130  REVMSAIAHFPGTVEGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 1012 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
            + ++  +A               +           E+  +FS ++   +K++KA +K G 
Sbjct: 183  VPVKEGAAAEESDDEEDEESGDDEEEEGDGGPDPEEAARRFSAVAEQQEKVQKALKKHGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S+   +    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243  GSKQATEELAALAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303  DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483  EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            P+R   L+ FL+
Sbjct: 603  PTRSEHLRSFLD 614



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/599 (50%), Positives = 412/599 (68%), Gaps = 22/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPE I D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEGISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   ++++    ++ E++ G ID +  S         +     
Sbjct: 130 REVMSAIAHFPGTVEGILAEYNRVTTEGGRLAEVLSGYIDPDDGSV-------PDEAAAP 182

Query: 222 ILIESSSA---------------DLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
           + ++  +A               +           E+  +FS ++   +K++KA +K G 
Sbjct: 183 VPVKEGAAAEESDDEEDEESGDDEEEEGDGGPDPEEAARRFSAVAEQQEKVQKALKKHGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S+   +    ++   + I+   K  + L   +R+ ++++   E+ I+++ V    MPR 
Sbjct: 243 GSKQATEELAALAELFMPIKLVPKQYDALVTQVRDALDRLRAQERAIMQLCVRDARMPRA 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+++FP NEI+++W  +  K +  Y   L      I+  QQKL +L+ +  L L +++D
Sbjct: 303 DFLRLFPGNEIDMDWAADLAKGKAKYAEALGNLQGDIQRCQQKLADLEAECSLSLAEIKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S+
Sbjct: 483 EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 KEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|424925271|ref|ZP_18348632.1| RpoD [Pseudomonas fluorescens R124]
 gi|404306431|gb|EJZ60393.1| RpoD [Pseudomonas fluorescens R124]
          Length = 615

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 312/601 (51%), Positives = 423/601 (70%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14   LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134  SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKAAKAD 193

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ +     
Sbjct: 194  DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRHNKAAVAELLV 253

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254  LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314  DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 554  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 613

Query: 1428 E 1428
            +
Sbjct: 614  D 614



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 306/588 (52%), Positives = 414/588 (70%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LIKLG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  
Sbjct: 14  LIKLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADAD 73

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 74  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 134 SAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPIDAKAAKAD 193

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  ++   +  RKA +K G ++++ +     
Sbjct: 194 DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGRHNKAAVAELLV 253

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 254 LAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 313

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 314 DESWSDALAKGKSKYAEAIGRVQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 373

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 374 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 434 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 493

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 553

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|296107953|ref|YP_003619654.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
            Alcoy]
 gi|295649855|gb|ADG25702.1| RNA polymerase primary sigma factor [Legionella pneumophila 2300/99
            Alcoy]
          Length = 621

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 321/607 (52%), Positives = 422/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ + F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194  LLDVDEEDEDGEGGISDVDDGPNPEQAKVYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314  TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 552  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 611

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 612  LRSFLEG 618



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/593 (52%), Positives = 411/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ + F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194 LLDVDEEDEDGEGGISDVDDGPNPEQAKVYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314 TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 492 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|387895986|ref|YP_006326283.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens A506]
 gi|387163419|gb|AFJ58618.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens A506]
          Length = 615

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 422/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10   RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDKDSLML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190  AKADDDSDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKQAIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ FP
Sbjct: 250  ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 413/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D ++LML
Sbjct: 10  RIKELILLGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDKDSLML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  +S   +  RKA +K G  ++  I 
Sbjct: 190 AKADDDSDDDEAESSDDEEEAESGPDPVIAAQRFGAVSDQMEITRKALKKHGRGNKQAIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ + ++   E+ I+++ V    MPR  F++ FP
Sbjct: 250 ELVALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRDARMPRTDFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALEAETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D+
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRDV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|325273045|ref|ZP_08139355.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
 gi|324101818|gb|EGB99354.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. TJI-51]
          Length = 616

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 312/606 (51%), Positives = 424/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      ++   + G K  
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTAEGGRLSDVLSGYIDPDDNIAAPTDEVPVIGAKAP 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++   E       ++  E+ +       +  +F  ++       K  +K G N +  I
Sbjct: 190  AAKEESDEEDEESEGSDDEEETESGPDPVVAAQRFGAVNDQLQVTNKVLKKHGRNHKESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            +A   +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  EALQALADLFMPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 306/593 (51%), Positives = 415/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      ++   + G K  
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTAEGGRLSDVLSGYIDPDDNIAAPTDEVPVIGAKAP 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++   E       ++  E+ +       +  +F  ++       K  +K G N +  I
Sbjct: 190 AAKEESDEEDEESEGSDDEEETESGPDPVVAAQRFGAVNDQLQVTNKVLKKHGRNHKESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           +A   +++  + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 EALQALADLFMPIKLVPKQFEVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRMF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|284008589|emb|CBA75169.1| RNA polymerase sigma-70 factor [Arsenophonus nasoniae]
          Length = 622

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 309/611 (50%), Positives = 416/611 (68%), Gaps = 10/611 (1%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D +
Sbjct: 11   NPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDAD 70

Query: 888  TLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             L+L+   +D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 71   DLILAETATDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 130

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-------- 997
            RIE+G+  +  +++  P  I  +L    ++ K E ++ +I+ G +D N   +        
Sbjct: 131  RIEDGINQVQCSVAEYPEAIAYLLDQYQRVEKGETRLSDIIIGFVDPNAEEDLAPTATHI 190

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
              V+     N++E    +       +++       +  KFS +   +++     +K G N
Sbjct: 191  GSVLPEEALNDDEDEDKDEDEDSDDSDENNVDPELARQKFSELREQYERTSLEIQKSGRN 250

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              + I     +S      R   K  + L + +R+ + +V   E+ I+++ + +C MP+ +
Sbjct: 251  HANSIAEIEQLSEIFKQFRLIPKQFDYLVNNMRDMMERVRSQERLIMKLCIEQCKMPKKN 310

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE N+NW+     +   ++  L      I+   QKL  ++ +  L +  ++DI
Sbjct: 311  FITLFSGNETNVNWLAAAKAMNKPWSEKLVEVEEEIQRSLQKLQQIEEETGLTIEQVKDI 370

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 371  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 430

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 431  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPE 490

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 491  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 550

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 551  SATHEVLAGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 610

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 611  SRSEVLRSFLD 621



 Score =  584 bits (1505), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 302/598 (50%), Positives = 407/598 (68%), Gaps = 10/598 (1%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D +
Sbjct: 11  NPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDAD 70

Query: 98  TLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            L+L+   +D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 71  DLILAETATDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 130

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-------- 207
           RIE+G+  +  +++  P  I  +L    ++ K E ++ +I+ G +D N   +        
Sbjct: 131 RIEDGINQVQCSVAEYPEAIAYLLDQYQRVEKGETRLSDIIIGFVDPNAEEDLAPTATHI 190

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
             V+     N++E    +       +++       +  KFS +   +++     +K G N
Sbjct: 191 GSVLPEEALNDDEDEDKDEDEDSDDSDENNVDPELARQKFSELREQYERTSLEIQKSGRN 250

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             + I     +S      R   K  + L + +R+ + +V   E+ I+++ + +C MP+ +
Sbjct: 251 HANSIAEIEQLSEIFKQFRLIPKQFDYLVNNMRDMMERVRSQERLIMKLCIEQCKMPKKN 310

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE N+NW+     +   ++  L      I+   QKL  ++ +  L +  ++DI
Sbjct: 311 FITLFSGNETNVNWLAAAKAMNKPWSEKLVEVEEEIQRSLQKLQQIEEETGLTIEQVKDI 370

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 371 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 430

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 431 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPE 490

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 491 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 550

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 SATHEVLAGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608


>gi|312963434|ref|ZP_07777916.1| sigma-70 [Pseudomonas fluorescens WH6]
 gi|311282240|gb|EFQ60839.1| sigma-70 [Pseudomonas fluorescens WH6]
          Length = 616

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 315/618 (50%), Positives = 419/618 (67%), Gaps = 33/618 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10   RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 993
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 994  ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
                  ++        ++EE+   ES    +   Q          +F  +S   +  RKA
Sbjct: 190  AKADDDSDDDEAEASTDDEEEA--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238  LKKHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L 
Sbjct: 298  ARMPRTDFLRQFPGNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALENETGLT 357

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358  IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478  GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538  ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHP+R   L+ FL+
Sbjct: 598  LRKLRHPTRSEHLRSFLD 615



 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/605 (51%), Positives = 410/605 (67%), Gaps = 33/605 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML
Sbjct: 10  RIKELITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALML 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++  +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  ADADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------------ 203
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 204 ---FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
                 ++        ++EE+   ES    +   Q          +F  +S   +  RKA
Sbjct: 190 AKADDDSDDDEAEASTDDEEEA--ESGPDPIIAAQ----------RFGAVSDQMEITRKA 237

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +K G +++  I     ++   + I+   K  E L + +R+ + ++   E+ I+++ V  
Sbjct: 238 LKKHGRSNKQAIAELLALAELFMPIKLVPKQFEGLVERVRSALERLRAQERAIMQLCVRD 297

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  F++ FP NE++ +W D   K +  Y   + R  P I   QQKL  L+ +  L 
Sbjct: 298 ARMPRTDFLRQFPGNEVDESWSDALAKGKSKYAEAIGRLQPDIIRCQQKLTALENETGLT 357

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358 IAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 477

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D 
Sbjct: 478 GREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDV 537

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 538 ATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 621 LRKLR 625
           LRKLR
Sbjct: 598 LRKLR 602


>gi|148359903|ref|YP_001251110.1| RNA polymerase sigma 70 factor RpoD [Legionella pneumophila str.
            Corby]
 gi|148281676|gb|ABQ55764.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila str.
            Corby]
          Length = 619

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 321/607 (52%), Positives = 422/607 (69%), Gaps = 17/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 14   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 132  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 191

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ + F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 192  LLDVDEEDEDGEGGISDVDDGPNPEQAKVYFDELREAFEKAMKALKEHGRTNKKTVELLD 251

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 312  TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 490  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 550  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 609

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 610  LRSFLEG 616



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/593 (52%), Positives = 411/593 (69%), Gaps = 17/593 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 14  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 132 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 191

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ + F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 192 LLDVDEEDEDGEGGISDVDDGPNPEQAKVYFDELREAFEKAMKALKEHGRTNKKTVELLD 251

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L+W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 312 TDLSWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 490 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|443910001|gb|AGD80571.1| RNA polymerase sigma factor RpoD, partial [Pseudomonas chlororaphis]
          Length = 615

 Score =  598 bits (1541), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 310/605 (51%), Positives = 423/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL   ++++    ++ +++ G ID +      ++       +K 
Sbjct: 130  REVMGAIAHFPGTVEHILSEYNRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDSKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  + 
Sbjct: 190  AKADDENDDDDAEASDDEEEAESGPDPIIAAQRFGAVAEQMEITRKALKKHGREHKQALA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  EMLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+++  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALESETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  584 bits (1505), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/592 (51%), Positives = 414/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL   ++++    ++ +++ G ID +      ++       +K 
Sbjct: 130 REVMGAIAHFPGTVEHILSEYNRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDSKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  + 
Sbjct: 190 AKADDENDDDDAEASDDEEEAESGPDPIIAAQRFGAVAEQMEITRKALKKHGREHKQALA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 EMLALAELFMPIKLVPKQFEALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+++  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALESETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|333902137|ref|YP_004476010.1| RNA polymerase sigma-70 subunit RpoD [Pseudomonas fulva 12-X]
 gi|333117402|gb|AEF23916.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas fulva 12-X]
          Length = 615

 Score =  598 bits (1541), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 310/605 (51%), Positives = 421/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ A++  P T+  IL    +++    ++ E++ G ID +  S           + + 
Sbjct: 130  REVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEVLSGYIDPDDGSVPAEAAAPVPASSDD 189

Query: 1012 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +   +  ++ +          +L +F+ +S   +  +KA +K G +S+  I+
Sbjct: 190  KAEDKDDDEEDGDSDDEEEEGDGGPDPEEALRRFTAVSDQLEVAKKALKKHGRDSKQAIE 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  + L   +R  ++++   E+ I+++ V    MPR  F+++FP
Sbjct: 250  ELRLLAELFMPIKLVPKQYDALVVRVREALDRLRGQERAIMQLCVRDARMPRADFLRLFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++L+W  +  K +  Y   +      I+  QQKLI LQ +  L L +++DINR+M  
Sbjct: 310  GNEVDLDWAASLAKGKAKYAEAIGNLEADIQRCQQKLIALQDETELTLAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  584 bits (1505), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/592 (51%), Positives = 412/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ A++  P T+  IL    +++    ++ E++ G ID +  S           + + 
Sbjct: 130 REVMGAVAHFPGTVDSILAEYTRVTTEGGRLVEVLSGYIDPDDGSVPAEAAAPVPASSDD 189

Query: 222 ILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +   +  ++ +          +L +F+ +S   +  +KA +K G +S+  I+
Sbjct: 190 KAEDKDDDEEDGDSDDEEEEGDGGPDPEEALRRFTAVSDQLEVAKKALKKHGRDSKQAIE 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  + L   +R  ++++   E+ I+++ V    MPR  F+++FP
Sbjct: 250 ELRLLAELFMPIKLVPKQYDALVVRVREALDRLRGQERAIMQLCVRDARMPRADFLRLFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++L+W  +  K +  Y   +      I+  QQKLI LQ +  L L +++DINR+M  
Sbjct: 310 GNEVDLDWAASLAKGKAKYAEAIGNLEADIQRCQQKLIALQDETELTLAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|429211562|ref|ZP_19202727.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. M1]
 gi|428156044|gb|EKX02592.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. M1]
          Length = 616

 Score =  598 bits (1541), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 312/614 (50%), Positives = 420/614 (68%), Gaps = 25/614 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AETDTDEAAAEEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P  +  IL    ++     ++ +I+ G ID +         G+    E +
Sbjct: 130  REVMSAIAQFPGAVDGILDEYQRVVSEGGRLSDILSGYIDPD--------DGSVPAEEVE 181

Query: 1012 ILIESSSADLSTEQLEKLKY-----------------ESLIKFSNISFHFDKMRKAFEKE 1054
            + ++    D   +  E+                    E+  +F  ++   DK +KA +K 
Sbjct: 182  LDLKDKGGDAKAKDDEEEDEESDDDSEDEGDGGPDPEEAARRFGLVADQLDKTKKALKKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  S+        ++   + I+   K  + L   +R+ ++QV + E+ I+++ V    MP
Sbjct: 242  GRGSKQADAEMLALAELFMPIKLVPKQFDALVTRVRDALDQVRRQERAIMQLCVRDARMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R  F+++FP  E +  WVD+  K +  Y   L R    +   QQKL  L++++ L ++++
Sbjct: 302  RADFLRLFPGRETDEAWVDSVLKAKPKYAEALERVKDDVIRNQQKLSALESNVDLKVSEI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +D+NR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  KDVNRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + 
Sbjct: 482  TPEELGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATSE 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSEHLRSFLD 615



 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/601 (50%), Positives = 411/601 (68%), Gaps = 25/601 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AETDTDEAAAEEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P  +  IL    ++     ++ +I+ G ID +         G+    E +
Sbjct: 130 REVMSAIAQFPGAVDGILDEYQRVVSEGGRLSDILSGYIDPD--------DGSVPAEEVE 181

Query: 222 ILIESSSADLSTEQLEKLKY-----------------ESLIKFSNISFHFDKMRKAFEKE 264
           + ++    D   +  E+                    E+  +F  ++   DK +KA +K 
Sbjct: 182 LDLKDKGGDAKAKDDEEEDEESDDDSEDEGDGGPDPEEAARRFGLVADQLDKTKKALKKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  S+        ++   + I+   K  + L   +R+ ++QV + E+ I+++ V    MP
Sbjct: 242 GRGSKQADAEMLALAELFMPIKLVPKQFDALVTRVRDALDQVRRQERAIMQLCVRDARMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R  F+++FP  E +  WVD+  K +  Y   L R    +   QQKL  L++++ L ++++
Sbjct: 302 RADFLRLFPGRETDEAWVDSVLKAKPKYAEALERVKDDVIRNQQKLSALESNVDLKVSEI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +D+NR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 KDVNRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +  +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + 
Sbjct: 482 TPEELGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEVATSE 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|384228081|ref|YP_005619816.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Ua
            (Uroleucon ambrosiae)]
 gi|345539014|gb|AEO07881.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Ua
            (Uroleucon ambrosiae)]
          Length = 608

 Score =  598 bits (1541), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 322/620 (51%), Positives = 425/620 (68%), Gaps = 33/620 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT+SE+ND LPEDIID E I  II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLITHGKEQGYLTYSEVNDHLPEDIIDSEQINDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNR 999
            AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N    FS    
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLDQYDRVKTGQIRLSDIITGFVDPNAEEIFSPTAL 181

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
             I       E+    +  + +       +L  E   KFS +   ++   K  + +    E
Sbjct: 182  HIGSELLEEEQNNEEDHENHEDDHSIDPELANE---KFSALRMQYNNTNKTIKNKNRKHE 238

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
              +    ++S      R   K  + L + +RN + +V + E+ I+++ V+ C MP+ +F+
Sbjct: 239  DSLLEIYHLSEIFKQFRLVPKQFDHLVNNMRNMMERVRKQERIIIKLCVDICKMPKKNFL 298

Query: 1120 KVFP-----------ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            K+FP           E   N  W +N TK+Q D  +       SIK    KLI ++ +  
Sbjct: 299  KIFPVQNIDHVWFIQEQNKNQPWSENLTKVQDDVFI-------SIK----KLIEIEKETG 347

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  ++DIN++M  GE+KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 348  LTIEQVKDINKRMSIGELKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 407

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 408  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 467

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 468  EIGREPTPEELSEKMFIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPL 527

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 528  DSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 587

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   L+ FL+
Sbjct: 588  KALRKLRHPSRSEVLRSFLD 607



 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 416/607 (68%), Gaps = 33/607 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT+SE+ND LPEDIID E I  II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLITHGKEQGYLTYSEVNDHLPEDIIDSEQINDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNR 209
           AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N    FS    
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLDQYDRVKTGQIRLSDIITGFVDPNAEEIFSPTAL 181

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
            I       E+    +  + +       +L  E   KFS +   ++   K  + +    E
Sbjct: 182 HIGSELLEEEQNNEEDHENHEDDHSIDPELANE---KFSALRMQYNNTNKTIKNKNRKHE 238

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
             +    ++S      R   K  + L + +RN + +V + E+ I+++ V+ C MP+ +F+
Sbjct: 239 DSLLEIYHLSEIFKQFRLVPKQFDHLVNNMRNMMERVRKQERIIIKLCVDICKMPKKNFL 298

Query: 330 KVFP-----------ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           K+FP           E   N  W +N TK+Q D  +       SIK    KLI ++ +  
Sbjct: 299 KIFPVQNIDHVWFIQEQNKNQPWSENLTKVQDDVFI-------SIK----KLIEIEKETG 347

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  ++DIN++M  GE+KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 348 LTIEQVKDINKRMSIGELKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 407

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 408 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 467

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 468 EIGREPTPEELSEKMFIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPL 527

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 528 DSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 587

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 588 KALRKLR 594


>gi|126666520|ref|ZP_01737498.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
 gi|126628908|gb|EAZ99527.1| RNA polymerase sigma factor RpoD [Marinobacter sp. ELB17]
          Length = 616

 Score =  598 bits (1541), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 314/609 (51%), Positives = 418/609 (68%), Gaps = 6/609 (0%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D +TL
Sbjct: 7    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTL 66

Query: 890  MLSNITSDDDVEEATEAALST--VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++++  S  D     EAA +   V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67   IMTDGDSTADEAATAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 1003
            EEG++D++ A++  P T   ++   D+I +NE ++ +IV G +D +    F         
Sbjct: 127  EEGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIVAGFLDPDDAEPFMPEEPAPAA 186

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              +  E     ++  A+    +      E+ ++F  +        +  E+ G + +   K
Sbjct: 187  PASAEESDSDDDADDAEEEETESGPDPEETRLRFGLLKEKLAVADELLEQHGRSDKRTQK 246

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A N +       +   K+ + L + +R+  + + Q E+ I+ I + +  M R  FIK FP
Sbjct: 247  ALNELGAVFAPFKLGNKAFDGLVNVVRSTNDMIRQNERTIMRICIRESKMDRKEFIKSFP 306

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NEINL+W +   + +  Y   +   +  I  LQ+++ N+Q ++ L + D+++INR++  
Sbjct: 307  GNEINLDWAEKIARSKKPYASAISERLDEIVRLQKRIKNVQLEVALDVVDIKEINRRVSI 366

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 547  LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606

Query: 1424 KIFLEGKKN 1432
            + F++ + N
Sbjct: 607  RGFIDDQGN 615



 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/600 (51%), Positives = 410/600 (68%), Gaps = 7/600 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D +TL
Sbjct: 7   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVSEVAPDADTL 66

Query: 100 MLSNITSDDDVEEATEAALST--VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++++  S  D     EAA +   V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67  IMTDGDSTADEAATAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 213
           EEG++D++ A++  P T   ++   D+I +NE ++ +IV G +D +    F         
Sbjct: 127 EEGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIVAGFLDPDDAEPFMPEEPAPAA 186

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
             +  E     ++  A+    +      E+ ++F  +        +  E+ G + +   K
Sbjct: 187 PASAEESDSDDDADDAEEEETESGPDPEETRLRFGLLKEKLAVADELLEQHGRSDKRTQK 246

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A N +       +   K+ + L + +R+  + + Q E+ I+ I + +  M R  FIK FP
Sbjct: 247 ALNELGAVFAPFKLGNKAFDGLVNVVRSTNDMIRQNERTIMRICIRESKMDRKEFIKSFP 306

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NEINL+W +   + +  Y   +   +  I  LQ+++ N+Q ++ L + D+++INR++  
Sbjct: 307 GNEINLDWAEKIARSKKPYASAISERLDEIVRLQKRIKNVQLEVALDVVDIKEINRRVSI 366

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 547 LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606


>gi|37527834|ref|NP_931179.1| RNA polymerase sigma factor RpoD [Photorhabdus luminescens subsp.
            laumondii TTO1]
 gi|36787270|emb|CAE16351.1| RNA polymerase sigma factor rpoD (Sigma-70) [Photorhabdus luminescens
            subsp. laumondii TTO1]
          Length = 614

 Score =  597 bits (1540), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 316/621 (50%), Positives = 422/621 (67%), Gaps = 29/621 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + LML+   +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLMLAETANDTD-EDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS---SNNRV 1000
            AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +    
Sbjct: 122  AKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEELAPTAT 181

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKE 1054
              G++   EE  L +    D      +     S+       KF  +   +D  R+  ++ 
Sbjct: 182  HVGSELPQEE--LDDDEDDDDEDSDDDSDDDNSIDPELARQKFQELRQQYDITRQEIKEN 239

Query: 1055 GYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            G N       H N + E+L +       R   K  + L + +R+ +++V   E+QI+++ 
Sbjct: 240  GRN-------HPNTAAEILKLSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMC 292

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V +C MP+ +FI +F  NE +  W      +   ++  L      ++   QKL  ++ + 
Sbjct: 293  VEQCKMPKKNFITLFSGNETSDIWFTAAKAMNKPWSEKLLEVEDEVQRSLQKLRQIEEET 352

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353  GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473  QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533  LDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 593  AKALRKLRHPSRSEVLRSFLD 613



 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 413/608 (67%), Gaps = 29/608 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + LML+   +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLMLAETANDTD-EDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS---SNNRV 210
           AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +    
Sbjct: 122 AKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEELAPTAT 181

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKE 264
             G++   EE  L +    D      +     S+       KF  +   +D  R+  ++ 
Sbjct: 182 HVGSELPQEE--LDDDEDDDDEDSDDDSDDDNSIDPELARQKFQELRQQYDITRQEIKEN 239

Query: 265 GYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           G N       H N + E+L +       R   K  + L + +R+ +++V   E+QI+++ 
Sbjct: 240 GRN-------HPNTAAEILKLSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMC 292

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V +C MP+ +FI +F  NE +  W      +   ++  L      ++   QKL  ++ + 
Sbjct: 293 VEQCKMPKKNFITLFSGNETSDIWFTAAKAMNKPWSEKLLEVEDEVQRSLQKLRQIEEET 352

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353 GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473 QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533 LDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 593 AKALRKLR 600


>gi|406943107|gb|EKD75179.1| hypothetical protein ACD_44C00206G0018 [uncultured bacterium]
          Length = 639

 Score =  597 bits (1540), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 316/632 (50%), Positives = 428/632 (67%), Gaps = 34/632 (5%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE---IIESIIKTFRYMDISVSE 881
            +IE+ R + K LI  GKE+G+LT+++I D LP  I   +   I++ I K  R M+I+V E
Sbjct: 3    DIESQRLQLKQLIASGKEQGHLTYADICDHLPPHIPAEQMKDIVKDIAKMLREMNINVYE 62

Query: 882  HVLDTETLMLSNITSDDDVEEATEAALSTV-------DSDFGRTKDPIKMYMREMGSVEL 934
               + ETL LS   S  + E   E               +FG   DP++MYMREMG+VEL
Sbjct: 63   SASEAETLPLSEEVSHPEEEADEEVVEQAAAVVLAAASDEFGGGNDPVRMYMREMGTVEL 122

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI-DKN 993
            LTR GEI IAKRIEEG+K +++A+      I +IL   D+    E ++ ++++G I D+ 
Sbjct: 123  LTRAGEIVIAKRIEEGMKQVMNALCQYSENISDILHEYDRTKTEEFRLSDLINGFILDET 182

Query: 994  FSSNNRV-----IKGNKNNNEEKILIESSS---ADLSTEQ---------LEKLKYESLIK 1036
            F     +     IK  K   +  + +  ++   A+ +TE+         L K K+++L  
Sbjct: 183  FQETENLPPELEIKAAKEEEDVVVALPETADEDAEGTTEEDPEGGPDPVLAKTKFDALRD 242

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
               ++   +K      K G N++  I+    ++   +  +   +  ++L   +R  ++QV
Sbjct: 243  LYEVTLKLEK------KHGRNNKKAIQQREKLATLFMEFKLIPRQFDRLMRKMRGMLDQV 296

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
             + E+ ++ + VN C M R HFI  FP+NE NLNWV  +  ++ +++  L  +   +  +
Sbjct: 297  RECERGVMNVCVNDCNMLRKHFIDSFPKNEANLNWVKTQINLKKEFSPALKEHQDEVIRI 356

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            Q+KL  ++    L + ++++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 357  QKKLQAIEEKTNLSIQEIKEINRQISIGETKARRAKKEMVEANLRLVISIAKKYTNRGLQ 416

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 417  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 476

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQILQETG EP P V+A+KMEM E+K+RKI+KIAKEP+SME+P+GDDEDSHLG
Sbjct: 477  NKLNRISRQILQETGQEPTPEVLALKMEMFEDKVRKILKIAKEPISMETPIGDDEDSHLG 536

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED N+ +P D+A+N  +R   + +L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 537  DFIEDANLFSPLDSAINEGLREATRQVLTSLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 596

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DVTRERIRQIEAKALRK+RHPSR   L+ FLE
Sbjct: 597  DVTRERIRQIEAKALRKMRHPSRAELLRSFLE 628



 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/619 (49%), Positives = 419/619 (67%), Gaps = 34/619 (5%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHE---IIESIIKTFRYMDISVSE 91
           +IE+ R + K LI  GKE+G+LT+++I D LP  I   +   I++ I K  R M+I+V E
Sbjct: 3   DIESQRLQLKQLIASGKEQGHLTYADICDHLPPHIPAEQMKDIVKDIAKMLREMNINVYE 62

Query: 92  HVLDTETLMLSNITSDDDVEEATEAALSTV-------DSDFGRTKDPIKMYMREMGSVEL 144
              + ETL LS   S  + E   E               +FG   DP++MYMREMG+VEL
Sbjct: 63  SASEAETLPLSEEVSHPEEEADEEVVEQAAAVVLAAASDEFGGGNDPVRMYMREMGTVEL 122

Query: 145 LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI-DKN 203
           LTR GEI IAKRIEEG+K +++A+      I +IL   D+    E ++ ++++G I D+ 
Sbjct: 123 LTRAGEIVIAKRIEEGMKQVMNALCQYSENISDILHEYDRTKTEEFRLSDLINGFILDET 182

Query: 204 FSSNNRV-----IKGNKNNNEEKILIESSS---ADLSTEQ---------LEKLKYESLIK 246
           F     +     IK  K   +  + +  ++   A+ +TE+         L K K+++L  
Sbjct: 183 FQETENLPPELEIKAAKEEEDVVVALPETADEDAEGTTEEDPEGGPDPVLAKTKFDALRD 242

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 306
              ++   +K      K G N++  I+    ++   +  +   +  ++L   +R  ++QV
Sbjct: 243 LYEVTLKLEK------KHGRNNKKAIQQREKLATLFMEFKLIPRQFDRLMRKMRGMLDQV 296

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
            + E+ ++ + VN C M R HFI  FP+NE NLNWV  +  ++ +++  L  +   +  +
Sbjct: 297 RECERGVMNVCVNDCNMLRKHFIDSFPKNEANLNWVKTQINLKKEFSPALKEHQDEVIRI 356

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
           Q+KL  ++    L + ++++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 357 QKKLQAIEEKTNLSIQEIKEINRQISIGETKARRAKKEMVEANLRLVISIAKKYTNRGLQ 416

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 417 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 476

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQILQETG EP P V+A+KMEM E+K+RKI+KIAKEP+SME+P+GDDEDSHLG
Sbjct: 477 NKLNRISRQILQETGQEPTPEVLALKMEMFEDKVRKILKIAKEPISMETPIGDDEDSHLG 536

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED N+ +P D+A+N  +R   + +L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 537 DFIEDANLFSPLDSAINEGLREATRQVLTSLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 596

Query: 607 DVTRERIRQIEAKALRKLR 625
           DVTRERIRQIEAKALRK+R
Sbjct: 597 DVTRERIRQIEAKALRKMR 615


>gi|443469986|ref|ZP_21060124.1| RNA polymerase sigma factor RpoD [Pseudomonas pseudoalcaligenes
            KF707]
 gi|442899505|gb|ELS25953.1| RNA polymerase sigma factor RpoD [Pseudomonas pseudoalcaligenes
            KF707]
          Length = 617

 Score =  597 bits (1540), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 317/609 (52%), Positives = 428/609 (70%), Gaps = 14/609 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------FSSNNR 999
            ++++ AI+  P  +  IL    +++    ++ ++++G ID +               +N 
Sbjct: 130  REVMSAIAHFPGAVDGILSEYHRVTTEGGRLSDVLNGYIDPDDGTLPAEEVEPELKDDNA 189

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
              K   ++ E++      S D      +    E+L +F+ +S   +K +KA +K G +S+
Sbjct: 190  AAKTKDDDEEDEEGESDDSEDEGDGGPDP--EEALRRFTAVSEQLEKAKKALKKHGRSSK 247

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
              I     ++   + I+   K  + L + +R+ +++V   E+ I+++ V    MPR  F+
Sbjct: 248  EAIAELLALAELFMPIKLVPKQFDALVEKVRSALDRVRAQERAIMQLCVRDARMPRADFL 307

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            ++FP NE++L W D     +  Y   + R    IK  QQKL++L+ ++ L +N+++DINR
Sbjct: 308  RLFPGNEVDLTWADGLASGKAKYAEAIGRLSDDIKRNQQKLVDLEQEVELTVNEIKDINR 367

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 368  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 427

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 428  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 487

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
              +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 488  GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 547

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 548  TREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 607

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 608  SEHLRSFLD 616



 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/596 (52%), Positives = 419/596 (70%), Gaps = 14/596 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------FSSNNR 209
           ++++ AI+  P  +  IL    +++    ++ ++++G ID +               +N 
Sbjct: 130 REVMSAIAHFPGAVDGILSEYHRVTTEGGRLSDVLNGYIDPDDGTLPAEEVEPELKDDNA 189

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
             K   ++ E++      S D      +    E+L +F+ +S   +K +KA +K G +S+
Sbjct: 190 AAKTKDDDEEDEEGESDDSEDEGDGGPDP--EEALRRFTAVSEQLEKAKKALKKHGRSSK 247

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
             I     ++   + I+   K  + L + +R+ +++V   E+ I+++ V    MPR  F+
Sbjct: 248 EAIAELLALAELFMPIKLVPKQFDALVEKVRSALDRVRAQERAIMQLCVRDARMPRADFL 307

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           ++FP NE++L W D     +  Y   + R    IK  QQKL++L+ ++ L +N+++DINR
Sbjct: 308 RLFPGNEVDLTWADGLASGKAKYAEAIGRLSDDIKRNQQKLVDLEQEVELTVNEIKDINR 367

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 368 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 427

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 428 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 487

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++  
Sbjct: 488 GERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEA 547

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 TREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|386818272|ref|ZP_10105490.1| RNA polymerase, sigma 70 subunit, RpoD [Thiothrix nivea DSM 5205]
 gi|386422848|gb|EIJ36683.1| RNA polymerase, sigma 70 subunit, RpoD [Thiothrix nivea DSM 5205]
          Length = 625

 Score =  597 bits (1539), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 315/618 (50%), Positives = 426/618 (68%), Gaps = 22/618 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  +   K LI  GKE+GYLT++E+ND LP+ I+D E IE I+     M I+V EH  D 
Sbjct: 5    EQQQSSLKELIARGKEQGYLTYAEVNDHLPDTIVDPEQIEDIVAMINDMGITVYEHAPDA 64

Query: 887  ETLMLSNITSDDDVEEATEAALS------TVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            ++L+L+    DD V+   EAA         VDSDFGRT DP++MYMREMG+VELLTR+GE
Sbjct: 65   DSLLLN----DDAVQADDEAAEEAAAALANVDSDFGRTTDPVRMYMREMGTVELLTREGE 120

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FS 995
            I+IA RIEEGL +++ A++  P +   +L  ++ I   EI++ +I++G ++ N     F+
Sbjct: 121  IQIAIRIEEGLNEILRALAQYPASTEVLLEKSELIDSEEIRLTDIINGFVNPNEDLNVFA 180

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKA 1050
                V+        E      +  D   E  + +       E+ IKF+ +   ++  + A
Sbjct: 181  VAAPVVDEEAAAAAEADDEAGTDEDDDDEASDPVDTGPDPEEARIKFAELRDLYEASKVA 240

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             +    N  +Y  A + ++ + +  R     I++L   L   ++++ Q E+ I+++ V K
Sbjct: 241  CDSN--NESAYTAARDAVATKFMEFRLAQPIIDQLTIQLNEIVDRIRQNERHIMKLCVQK 298

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             GM R  FI  FP+NE +L W++     +      L   +P ++E Q++L+ ++ +  L 
Sbjct: 299  GGMARQDFIDSFPQNETDLEWLNRYCADKRGDTSKLLALLPKVREAQEQLLEIERECNLS 358

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DINR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 359  IAQIKDINRSMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 418

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR++LQE 
Sbjct: 419  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRKLLQEK 478

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A  M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+L+P ++
Sbjct: 479  GREATPEELAEAMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNILSPIES 538

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A  +S+  + +++L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 539  ATTSSLSEITREVLSSLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 598

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FLE
Sbjct: 599  LRKLRHPSRSDMLRSFLE 616



 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/613 (50%), Positives = 420/613 (68%), Gaps = 23/613 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  +   K LI  GKE+GYLT++E+ND LP+ I+D E IE I+     M I+V EH  D 
Sbjct: 5   EQQQSSLKELIARGKEQGYLTYAEVNDHLPDTIVDPEQIEDIVAMINDMGITVYEHAPDA 64

Query: 97  ETLMLSNITSDDDVEEATEAALS------TVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           ++L+L+    DD V+   EAA         VDSDFGRT DP++MYMREMG+VELLTR+GE
Sbjct: 65  DSLLLN----DDAVQADDEAAEEAAAALANVDSDFGRTTDPVRMYMREMGTVELLTREGE 120

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FS 205
           I+IA RIEEGL +++ A++  P +   +L  ++ I   EI++ +I++G ++ N     F+
Sbjct: 121 IQIAIRIEEGLNEILRALAQYPASTEVLLEKSELIDSEEIRLTDIINGFVNPNEDLNVFA 180

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKA 260
               V+        E      +  D   E  + +       E+ IKF+ +   ++  + A
Sbjct: 181 VAAPVVDEEAAAAAEADDEAGTDEDDDDEASDPVDTGPDPEEARIKFAELRDLYEASKVA 240

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            +    N  +Y  A + ++ + +  R     I++L   L   ++++ Q E+ I+++ V K
Sbjct: 241 CDSN--NESAYTAARDAVATKFMEFRLAQPIIDQLTIQLNEIVDRIRQNERHIMKLCVQK 298

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            GM R  FI  FP+NE +L W++     +      L   +P ++E Q++L+ ++ +  L 
Sbjct: 299 GGMARQDFIDSFPQNETDLEWLNRYCADKRGDTSKLLALLPKVREAQEQLLEIERECNLS 358

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DINR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 359 IAQIKDINRSMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 418

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR++LQE 
Sbjct: 419 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRKLLQEK 478

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A  M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+L+P ++
Sbjct: 479 GREATPEELAEAMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNILSPIES 538

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A  +S+  + +++L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 539 ATTSSLSEITREVLSSLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 598

Query: 621 LRKLR-PLAHDWL 632
           LRKLR P   D L
Sbjct: 599 LRKLRHPSRSDML 611


>gi|62181728|ref|YP_218145.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Choleraesuis str. SC-B67]
 gi|375116068|ref|ZP_09761238.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Choleraesuis str. SCSA50]
 gi|62129361|gb|AAX67064.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Salmonella enterica subsp.
            enterica serovar Choleraesuis str. SC-B67]
 gi|322716214|gb|EFZ07785.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Choleraesuis str. SCSA50]
          Length = 658

 Score =  597 bits (1539), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 314/653 (48%), Positives = 430/653 (65%), Gaps = 16/653 (2%)

Query: 792  DKYDPDSYIR----KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKER 843
            D+  PDS       K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEE 244

Query: 1022 STEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 1075
              +        S+       KF+ +   +   R   + +G +  +  K    +S      
Sbjct: 245  DGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQKEILKLSEVFKQF 304

Query: 1076 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 1135
            R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +  
Sbjct: 305  RLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAA 364

Query: 1136 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 1195
              +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM
Sbjct: 365  IAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEM 424

Query: 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255
             EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 425  VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 484

Query: 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315
            TRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++K
Sbjct: 485  TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLK 544

Query: 1316 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 1375
            IAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVL
Sbjct: 545  IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVL 604

Query: 1376 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 657



 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/635 (47%), Positives = 420/635 (66%), Gaps = 14/635 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEEDGDDD 249

Query: 237 EKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
                 S+       KF+ +   +   R   + +G +  +  K    +S      R   K
Sbjct: 250 AADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQKEILKLSEVFKQFRLVPK 309

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
             + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +  
Sbjct: 310 QFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNK 369

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANL
Sbjct: 370 PWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANL 429

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 430 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 489

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP
Sbjct: 490 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEP 549

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMRFG
Sbjct: 550 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFG 609

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 644


>gi|388543056|ref|ZP_10146348.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. M47T1]
 gi|388279142|gb|EIK98712.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. M47T1]
          Length = 615

 Score =  597 bits (1538), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 314/605 (51%), Positives = 418/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------FSSNNRVIKG 1003
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +                  
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAP 189

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
             K  +++      SS D    +       +  +F  +S   D   KA +K G +S+  I 
Sbjct: 190  AKAESDDDEEESDSSDDEEETESGPDPVVAAQRFGAVSEQLDITLKALKKHGRDSKQGIA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++     I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F+++FP
Sbjct: 250  EMLALAELFQPIKLVPKQFEVLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRLFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE+++ W  +  K    +   L R    I   QQKL++L+T+  L + +++DINR+M  
Sbjct: 310  SNEVDMTWAGDLAKRSTKWAEALGRLNADIVRCQQKLVDLETETGLTIVEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/592 (52%), Positives = 409/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--------FSSNNRVIKG 213
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +                  
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAP 189

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
            K  +++      SS D    +       +  +F  +S   D   KA +K G +S+  I 
Sbjct: 190 AKAESDDDEEESDSSDDEEETESGPDPVVAAQRFGAVSEQLDITLKALKKHGRDSKQGIA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++     I+   K  E L + +R  ++++ Q E+ I+++ V    MPR  F+++FP
Sbjct: 250 EMLALAELFQPIKLVPKQFEVLVERVRGALDRLRQQERAIMQLCVRDARMPRADFLRLFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE+++ W  +  K    +   L R    I   QQKL++L+T+  L + +++DINR+M  
Sbjct: 310 SNEVDMTWAGDLAKRSTKWAEALGRLNADIVRCQQKLVDLETETGLTIVEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|379009538|ref|YP_005267351.1| RNA polymerase, sigma 70 (sigma D) factor [Wigglesworthia glossinidia
            endosymbiont of Glossina morsitans morsitans (Yale
            colony)]
 gi|375158062|gb|AFA41128.1| RNA polymerase, sigma 70 (sigma D) factor [Wigglesworthia glossinidia
            endosymbiont of Glossina morsitans morsitans (Yale
            colony)]
          Length = 606

 Score =  597 bits (1538), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 316/614 (51%), Positives = 421/614 (68%), Gaps = 23/614 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTFSE+ND LPE+I+D   I+ II+    M I V +   D 
Sbjct: 3    KNQQSQLKLLVTRGKEQGYLTFSEVNDHLPENILDSHQIDDIIQMITDMGIQVMDEAPDP 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L N T   D+DV E     LS V+SDFGRT DP++MYMREMGSVELLTR+GEI +A
Sbjct: 63   DNLLLPNSTENLDEDVAEVAAQVLSNVESDFGRTTDPVRMYMREMGSVELLTREGEINLA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  +L   + I K E+++ +++ G ID N S +   I   
Sbjct: 123  KRIEDGINQVQCSVAEYPETITYLLKQYNFILKGELRLSDLITGFIDPNISMDAAAISAT 182

Query: 1005 --KNNNEEKILIESS--------SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 1054
               + + E+I ++            +L+ ++  +L+ +  I +++I  H           
Sbjct: 183  IISDLSAEEISVDDHHVTDENNIDVELAHQKFLELQQQYDITYNSIHIH----------- 231

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G N  + IK    +++     RF  K  + L   +R  I ++   E++I+++ V+   MP
Sbjct: 232  GRNHVNSIKEITKLADLFKQFRFVPKQFDCLVHIIRAVIAKIRIHERRIMQLCVSVGKMP 291

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  FI +F   E N NW+     +   ++  L +   SI     KL  ++ +  L +   
Sbjct: 292  KKSFIALFTGCETNENWLKKALSLNKSWSKTLNKLYHSIYFSINKLKLIENETGLTIKQA 351

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR++  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 352  KDINRRISLGEEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 411

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 412  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREP 471

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  ++ KM MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++  P D+A + 
Sbjct: 472  TPEELSEKMFMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSLDLPLDSATSE 531

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   D+L+ LTPRE+KVLRMRFGI+MS+DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 532  SLRSATHDVLSGLTPREAKVLRMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 591

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 592  RHPSRSEILRSFLD 605



 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/601 (51%), Positives = 412/601 (68%), Gaps = 23/601 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTFSE+ND LPE+I+D   I+ II+    M I V +   D 
Sbjct: 3   KNQQSQLKLLVTRGKEQGYLTFSEVNDHLPENILDSHQIDDIIQMITDMGIQVMDEAPDP 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L N T   D+DV E     LS V+SDFGRT DP++MYMREMGSVELLTR+GEI +A
Sbjct: 63  DNLLLPNSTENLDEDVAEVAAQVLSNVESDFGRTTDPVRMYMREMGSVELLTREGEINLA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  +L   + I K E+++ +++ G ID N S +   I   
Sbjct: 123 KRIEDGINQVQCSVAEYPETITYLLKQYNFILKGELRLSDLITGFIDPNISMDAAAISAT 182

Query: 215 --KNNNEEKILIESS--------SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 264
              + + E+I ++            +L+ ++  +L+ +  I +++I  H           
Sbjct: 183 IISDLSAEEISVDDHHVTDENNIDVELAHQKFLELQQQYDITYNSIHIH----------- 231

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G N  + IK    +++     RF  K  + L   +R  I ++   E++I+++ V+   MP
Sbjct: 232 GRNHVNSIKEITKLADLFKQFRFVPKQFDCLVHIIRAVIAKIRIHERRIMQLCVSVGKMP 291

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  FI +F   E N NW+     +   ++  L +   SI     KL  ++ +  L +   
Sbjct: 292 KKSFIALFTGCETNENWLKKALSLNKSWSKTLNKLYHSIYFSINKLKLIENETGLTIKQA 351

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR++  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 352 KDINRRISLGEEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 411

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 412 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREP 471

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  ++ KM MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++  P D+A + 
Sbjct: 472 TPEELSEKMFMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSLDLPLDSATSE 531

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   D+L+ LTPRE+KVLRMRFGI+MS+DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 532 SLRSATHDVLSGLTPREAKVLRMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 591

Query: 625 R 625
           R
Sbjct: 592 R 592


>gi|293394293|ref|ZP_06638593.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
            DSM 4582]
 gi|291423271|gb|EFE96500.1| DNA-directed RNA polymerase sigma subunit RpoD [Serratia odorifera
            DSM 4582]
          Length = 647

 Score =  596 bits (1537), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 308/608 (50%), Positives = 423/608 (69%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 98

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 159  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 218

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ + EE+   E    D   E    +  E +  KF+ +   ++  R+  +  G +  S
Sbjct: 219  IGSELSTEEQSDDEEEDDDDDAEDDNSIDPELARQKFTELREQYEATRQVIKTNGRSHAS 278

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S+     R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 279  AAEEILKLSDVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKLCVEQCKMPKKNFVT 338

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 339  LFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTIEQVKDINRR 398

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 399  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 458

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 459  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 518

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 519  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 578

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 579  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 638

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 639  EVLRSFLD 646



 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 414/595 (69%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 98

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 159 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 218

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ + EE+   E    D   E    +  E +  KF+ +   ++  R+  +  G +  S
Sbjct: 219 IGSELSTEEQSDDEEEDDDDDAEDDNSIDPELARQKFTELREQYEATRQVIKTNGRSHAS 278

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S+     R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 279 AAEEILKLSDVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKLCVEQCKMPKKNFVT 338

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 339 LFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTIEQVKDINRR 398

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 399 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 458

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 459 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 518

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 519 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 578

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 579 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 633


>gi|170723972|ref|YP_001751660.1| RNA polymerase sigma factor RpoD [Pseudomonas putida W619]
 gi|169761975|gb|ACA75291.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudomonas putida W619]
          Length = 616

 Score =  596 bits (1537), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 311/606 (51%), Positives = 416/606 (68%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 1010 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
                      +      ++ + ES         +F  +S       K  +K G +    I
Sbjct: 190  AAKEEADDEEESDDSSDDEEETESGPDPVVAAQRFGAVSDQLAITLKVLKKHGRSHAESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   +++  + I+   K  + L + +R+ + ++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  GAMQALADLFMPIKLVPKQFDVLVERVRDALARLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + +++DINR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/593 (51%), Positives = 407/593 (68%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID   N ++    +        
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 220 EKILIESSSADLSTEQLEKLKYES-------LIKFSNISFHFDKMRKAFEKEGYNSESYI 272
                     +      ++ + ES         +F  +S       K  +K G +    I
Sbjct: 190 AAKEEADDEEESDDSSDDEEETESGPDPVVAAQRFGAVSDQLAITLKVLKKHGRSHAESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   +++  + I+   K  + L + +R+ + ++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 GAMQALADLFMPIKLVPKQFDVLVERVRDALARLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + +++DINR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|407792575|ref|ZP_11139612.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina xiamenensis
            10-D-4]
 gi|407217688|gb|EKE87520.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina xiamenensis
            10-D-4]
          Length = 614

 Score =  596 bits (1536), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 314/622 (50%), Positives = 421/622 (67%), Gaps = 32/622 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLTF+E+ND LP++I+D + IE II+    M I V E+  D 
Sbjct: 3    QNRQSQLKLLIAKGKEQGYLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIQVFENAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM+S   +D+D  E    AL++VDS+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMSESAADEDAAEEAAQALASVDSEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D     E+++ +I+ G ID N      V   +  
Sbjct: 123  IEDGINQVQCSVAEYPEAINFLLEQWDAFEAEEVRLTDIISGFIDPNEVDTAPVSATH-- 180

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI--------------------KFSNISFHFDK 1046
                        ++L+ EQL++   +                       KF+ +   ++ 
Sbjct: 181  ----------VGSELTDEQLKEDDEDEDDDDDDSDDDADTGIDPEFARQKFTELRDQYEA 230

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
             R+A +K G +        + +S      R   K  ++L   +R+ +++V   E+ I+++
Sbjct: 231  TRQAIQKHGRDHAKARTQIDELSELFKQFRLVPKQFDRLVKDMRDMMHRVRVQERLIMKL 290

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             + + GMP+  F++ F  NE NL+WVD +      Y   L      I+   +KL  ++ +
Sbjct: 291  SIEQGGMPKRQFMRAFAGNENNLSWVDEQVNSSESYAESLAAVRSEIERCVKKLAEVEEE 350

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 351  TGLTIAKVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 410

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 411  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 470

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 471  LQEMGREPLPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLDL 530

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A + S+R+ V+D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 531  PVDSATSESLRNAVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 590

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR  +LK FL+
Sbjct: 591  EAKALRKLRHPSRSEQLKSFLD 612



 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 411/609 (67%), Gaps = 32/609 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLTF+E+ND LP++I+D + IE II+    M I V E+  D 
Sbjct: 3   QNRQSQLKLLIAKGKEQGYLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIQVFENAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM+S   +D+D  E    AL++VDS+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMSESAADEDAAEEAAQALASVDSEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D     E+++ +I+ G ID N      V   +  
Sbjct: 123 IEDGINQVQCSVAEYPEAINFLLEQWDAFEAEEVRLTDIISGFIDPNEVDTAPVSATH-- 180

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI--------------------KFSNISFHFDK 256
                       ++L+ EQL++   +                       KF+ +   ++ 
Sbjct: 181 ----------VGSELTDEQLKEDDEDEDDDDDDSDDDADTGIDPEFARQKFTELRDQYEA 230

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
            R+A +K G +        + +S      R   K  ++L   +R+ +++V   E+ I+++
Sbjct: 231 TRQAIQKHGRDHAKARTQIDELSELFKQFRLVPKQFDRLVKDMRDMMHRVRVQERLIMKL 290

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            + + GMP+  F++ F  NE NL+WVD +      Y   L      I+   +KL  ++ +
Sbjct: 291 SIEQGGMPKRQFMRAFAGNENNLSWVDEQVNSSESYAESLAAVRSEIERCVKKLAEVEEE 350

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 351 TGLTIAKVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 410

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 411 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 470

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 471 LQEMGREPLPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLDL 530

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A + S+R+ V+D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 531 PVDSATSESLRNAVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 590

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 591 EAKALRKLR 599


>gi|395235398|ref|ZP_10413610.1| RNA polymerase sigma factor RpoD [Enterobacter sp. Ag1]
 gi|394729932|gb|EJF29847.1| RNA polymerase sigma factor RpoD [Enterobacter sp. Ag1]
          Length = 614

 Score =  596 bits (1536), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 304/611 (49%), Positives = 421/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
              +   +  ++    +      +    ++ I        F ++RK +E      ++  ++
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRKQYELTRDTIKAKGRS 242

Query: 1065 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            H + + E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HADAAAEILQLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHEVSEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 297/598 (49%), Positives = 412/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
             +   +  ++    +      +    ++ I        F ++RK +E      ++  ++
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRKQYELTRDTIKAKGRS 242

Query: 275 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           H + + E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HADAAAEILQLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHEVSEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|365847769|ref|ZP_09388251.1| RNA polymerase sigma factor RpoD [Yokenella regensburgei ATCC 43003]
 gi|364571625|gb|EHM49202.1| RNA polymerase sigma factor RpoD [Yokenella regensburgei ATCC 43003]
          Length = 614

 Score =  596 bits (1536), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEEEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDVIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAASQEEIQKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSDTWFNAAVAMNKPWSEKLHDVAEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEEEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDVIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAASQEEIQKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSDTWFNAAVAMNKPWSEKLHDVAEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|448243976|ref|YP_007408029.1| RNA polymerase, sigma 70 (sigma D) factor [Serratia marcescens WW4]
 gi|445214340|gb|AGE20010.1| RNA polymerase, sigma 70 (sigma D) factor [Serratia marcescens WW4]
 gi|453063601|gb|EMF04580.1| RNA polymerase sigma factor RpoD [Serratia marcescens VGH107]
          Length = 613

 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 306/617 (49%), Positives = 422/617 (68%), Gaps = 22/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
              +       +    D   E  +     S+       KF+ +   ++  R   +K G   
Sbjct: 183  IGSELSSEEQDDDEEDEDDEDDDTEDDNSIDPELARQKFAELRDQYEATRLVIKKNG--- 239

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H + ++E+L +       R   K  + L +++R  +++V   E+ I+++ V +C
Sbjct: 240  ----RSHASAADEILKLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKLCVEQC 295

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +
Sbjct: 296  KMPKKNFVTLFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTI 355

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 356  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 415

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 416  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 475

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 476  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 535

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 536  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 596  RKLRHPSRSEVLRSFLD 612



 Score =  581 bits (1498), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 299/604 (49%), Positives = 413/604 (68%), Gaps = 22/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
             +       +    D   E  +     S+       KF+ +   ++  R   +K G   
Sbjct: 183 IGSELSSEEQDDDEEDEDDEDDDTEDDNSIDPELARQKFAELRDQYEATRLVIKKNG--- 239

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H + ++E+L +       R   K  + L +++R  +++V   E+ I+++ V +C
Sbjct: 240 ----RSHASAADEILKLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKLCVEQC 295

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +
Sbjct: 296 KMPKKNFVTLFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTI 355

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 356 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 415

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 416 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 475

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 476 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 535

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 536 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 622 RKLR 625
           RKLR
Sbjct: 596 RKLR 599


>gi|224585014|ref|YP_002638813.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Paratyphi C strain RKS4594]
 gi|224469542|gb|ACN47372.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
            serovar Paratyphi C strain RKS4594]
          Length = 658

 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 313/653 (47%), Positives = 430/653 (65%), Gaps = 16/653 (2%)

Query: 792  DKYDPDSYIR----KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKER 843
            D+  PDS       K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEE 244

Query: 1022 STEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 1075
              +        S+       KF+ +   +   R   + +G +  +  +    +S      
Sbjct: 245  DGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQF 304

Query: 1076 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 1135
            R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +  
Sbjct: 305  RLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAA 364

Query: 1136 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 1195
              +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM
Sbjct: 365  IAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEM 424

Query: 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255
             EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 425  VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 484

Query: 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315
            TRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++K
Sbjct: 485  TRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLK 544

Query: 1316 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 1375
            IAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVL
Sbjct: 545  IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVL 604

Query: 1376 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 657



 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 303/635 (47%), Positives = 420/635 (66%), Gaps = 14/635 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEEDGDDD 249

Query: 237 EKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
                 S+       KF+ +   +   R   + +G +  +  +    +S      R   K
Sbjct: 250 AADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPK 309

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
             + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +  
Sbjct: 310 QFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNK 369

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANL
Sbjct: 370 PWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANL 429

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 430 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 489

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP
Sbjct: 490 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEP 549

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMRFG
Sbjct: 550 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFG 609

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 644


>gi|270263179|ref|ZP_06191449.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|333929232|ref|YP_004502811.1| RNA polymerase sigma-70 subunit RpoD [Serratia sp. AS12]
 gi|333934185|ref|YP_004507763.1| RNA polymerase sigma-70 subunit RpoD [Serratia plymuthica AS9]
 gi|386331055|ref|YP_006027225.1| RNA polymerase sigma-70 subunit RpoD [Serratia sp. AS13]
 gi|270042867|gb|EFA15961.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|333475792|gb|AEF47502.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia plymuthica AS9]
 gi|333493292|gb|AEF52454.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia sp. AS12]
 gi|333963388|gb|AEG30161.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia sp. AS13]
          Length = 648

 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 305/610 (50%), Positives = 421/610 (69%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 98

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 159  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 217

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E     ++   +   E  +     S+       KF+++   ++  R   +K G + 
Sbjct: 218  HVGSELSTEEQNDDEEDEDEDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 277

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 278  ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 337

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 338  VTLFAGNETSNSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 397

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 398  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 457

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 458  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 517

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 518  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 577

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 578  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 637

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 638  RSEVLRSFLD 647



 Score =  581 bits (1498), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 298/597 (49%), Positives = 412/597 (69%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39  QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 98

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 159 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 217

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E     ++   +   E  +     S+       KF+++   ++  R   +K G + 
Sbjct: 218 HVGSELSTEEQNDDEEDEDEDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 277

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 278 ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 337

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 338 VTLFAGNETSNSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 397

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 398 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 457

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 458 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 517

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 518 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 577

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 578 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 634


>gi|350421245|ref|XP_003492783.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Bombus impatiens]
          Length = 615

 Score =  595 bits (1535), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 318/618 (51%), Positives = 426/618 (68%), Gaps = 23/618 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL-D 885
            +N + + K+LI  GKE GYLT++++ND LPE+IID + IE II+    M I V E    D
Sbjct: 3    QNSKSQLKLLISRGKELGYLTYADLNDHLPEEIIDSDQIEDIIQMINDMGIQVLEEAPED 62

Query: 886  TETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            T+ L+L+   +D+D VE AT   LS V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   TDDLLLNGEVADEDAVEAATALVLSNVESEIGRTTDPVRMYMREMGAVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------SSNN 998
            KRIEEG+  +  ++S  P  I  +L   D + K+E+++ +I+ G +D N       +   
Sbjct: 123  KRIEEGINQVQSSVSEYPEAITYLLEQYDLVEKDELRLSDIITGFVDPNIDEALSDAPEE 182

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYN 1057
             + +   + ++     E +    +TE+   +  E +  KF  +    +K   A +K G  
Sbjct: 183  PIKEAEISLDDSDDEDEENEDSSATEEDSTIDPELARQKFVQLREQHEKTSAAIKKYGRG 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            ++   +   N+S      R   +  + L + +R  +++V   E+ I+ + V++  MP+  
Sbjct: 243  NKKAQQEIENLSEIFKQFRLVGRQFDILVNNMRQMMDRVRTHERVIMRLAVDQSKMPKKL 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK----ELQQKLINLQT---DIVLP 1170
            F+ +F  NE NL+W +   K +  Y       +P ++    E+ Q++  LQ    +  L 
Sbjct: 303  FMTLFAGNENNLSWFEKAIKSKAAY-------VPKLETFHDEITQQITLLQAIEVETNLS 355

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 356  IEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 415

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 416  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEI 475

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  ++ +M+MPE+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED +M  P DA
Sbjct: 476  GREPTPEELSERMQMPEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTSMELPLDA 535

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A + S+R    +IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 536  ATSESLRLATSEILEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 595

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FL+
Sbjct: 596  LRKLRHPSRSDVLRSFLD 613



 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 417/605 (68%), Gaps = 23/605 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL-D 95
           +N + + K+LI  GKE GYLT++++ND LPE+IID + IE II+    M I V E    D
Sbjct: 3   QNSKSQLKLLISRGKELGYLTYADLNDHLPEEIIDSDQIEDIIQMINDMGIQVLEEAPED 62

Query: 96  TETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           T+ L+L+   +D+D VE AT   LS V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  TDDLLLNGEVADEDAVEAATALVLSNVESEIGRTTDPVRMYMREMGAVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------SSNN 208
           KRIEEG+  +  ++S  P  I  +L   D + K+E+++ +I+ G +D N       +   
Sbjct: 123 KRIEEGINQVQSSVSEYPEAITYLLEQYDLVEKDELRLSDIITGFVDPNIDEALSDAPEE 182

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYN 267
            + +   + ++     E +    +TE+   +  E +  KF  +    +K   A +K G  
Sbjct: 183 PIKEAEISLDDSDDEDEENEDSSATEEDSTIDPELARQKFVQLREQHEKTSAAIKKYGRG 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           ++   +   N+S      R   +  + L + +R  +++V   E+ I+ + V++  MP+  
Sbjct: 243 NKKAQQEIENLSEIFKQFRLVGRQFDILVNNMRQMMDRVRTHERVIMRLAVDQSKMPKKL 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK----ELQQKLINLQT---DIVLP 380
           F+ +F  NE NL+W +   K +  Y       +P ++    E+ Q++  LQ    +  L 
Sbjct: 303 FMTLFAGNENNLSWFEKAIKSKAAY-------VPKLETFHDEITQQITLLQAIEVETNLS 355

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 356 IEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 415

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 416 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEI 475

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  ++ +M+MPE+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED +M  P DA
Sbjct: 476 GREPTPEELSERMQMPEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTSMELPLDA 535

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A + S+R    +IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 536 ATSESLRLATSEILEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 595

Query: 621 LRKLR 625
           LRKLR
Sbjct: 596 LRKLR 600


>gi|399543604|ref|YP_006556912.1| RNA polymerase sigma factor rpoD [Marinobacter sp. BSs20148]
 gi|399158936|gb|AFP29499.1| RNA polymerase sigma factor rpoD [Marinobacter sp. BSs20148]
          Length = 616

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 312/609 (51%), Positives = 417/609 (68%), Gaps = 6/609 (0%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V+E   D +TL
Sbjct: 7    KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVTEVAPDADTL 66

Query: 890  MLSNITSDDDVEEATEAALST--VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++++  S  D     EAA +   V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67   IMTDGDSTADEAATAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 1003
            EEG++D++ A++  P T   ++   D+I +NE ++ +IV G +D +    F         
Sbjct: 127  EEGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIVAGFLDPDDAEPFMPEEPAPAA 186

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              +  E     ++   +    +      E+ ++F  +        +  E+ G + +   K
Sbjct: 187  PASAEESDSDDDADDTEEEETESGPDPEETRLRFDLLKEKLAVAHELLEQHGRSDKRTQK 246

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A N +       +   K+ + L + +R+  + + Q E+ I+ I + +  M R  FIK FP
Sbjct: 247  ALNELGAVFAPFKLGNKAFDGLVNVVRSTNDMIRQNERTIMRICIRESKMDRKEFIKSFP 306

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NEINL+W +   + +  Y   +   +  I  LQ+++ N+Q ++ L + D+++INR++  
Sbjct: 307  GNEINLDWAEKIARSKKPYASAISERLDEIVRLQKRIKNVQLEVGLDVVDIKEINRRVSI 366

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 547  LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606

Query: 1424 KIFLEGKKN 1432
            + F++ + N
Sbjct: 607  RGFIDDQGN 615



 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/600 (51%), Positives = 409/600 (68%), Gaps = 7/600 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V+E   D +TL
Sbjct: 7   KSRLKDLIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIQVTEVAPDADTL 66

Query: 100 MLSNITSDDDVEEATEAALST--VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++++  S  D     EAA +   V+SD GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 67  IMTDGDSTADEAATAEAAAALAAVESDAGRTTDPVRMYMREMGTVELLTREGEIVIAKRI 126

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKG 213
           EEG++D++ A++  P T   ++   D+I +NE ++ +IV G +D +    F         
Sbjct: 127 EEGIRDVMAAVAHFPGTTGTVIQGYDRIVENEGRLSDIVAGFLDPDDAEPFMPEEPAPAA 186

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
             +  E     ++   +    +      E+ ++F  +        +  E+ G + +   K
Sbjct: 187 PASAEESDSDDDADDTEEEETESGPDPEETRLRFDLLKEKLAVAHELLEQHGRSDKRTQK 246

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A N +       +   K+ + L + +R+  + + Q E+ I+ I + +  M R  FIK FP
Sbjct: 247 ALNELGAVFAPFKLGNKAFDGLVNVVRSTNDMIRQNERTIMRICIRESKMDRKEFIKSFP 306

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NEINL+W +   + +  Y   +   +  I  LQ+++ N+Q ++ L + D+++INR++  
Sbjct: 307 GNEINLDWAEKIARSKKPYASAISERLDEIVRLQKRIKNVQLEVGLDVVDIKEINRRVSI 366

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 427 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 486

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED   L+P D+A    +R   + +
Sbjct: 487 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDIQALSPVDSATAEGLREATRSV 546

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RESKVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 547 LAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 606


>gi|399007377|ref|ZP_10709887.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM17]
 gi|425901948|ref|ZP_18878539.1| RNA polymerase sigma factor RpoD [Pseudomonas chlororaphis subsp.
            aureofaciens 30-84]
 gi|397892739|gb|EJL09216.1| RNA polymerase sigma factor RpoD [Pseudomonas chlororaphis subsp.
            aureofaciens 30-84]
 gi|398120349|gb|EJM10013.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM17]
          Length = 615

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 421/605 (69%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 1006
            ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130  REVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               +    +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  + 
Sbjct: 190  AKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGREHKQALA 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250  EMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310  GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 550  LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHL 609

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 610  RSFLD 614



 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/592 (51%), Positives = 412/592 (69%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKN 216
           ++++ AI+  P T+  IL    +++    ++ +++ G ID +      ++        K 
Sbjct: 130 REVMGAIAHFPGTVEHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              +    +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  + 
Sbjct: 190 AKADDDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGREHKQALA 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP
Sbjct: 250 EMLALAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFP 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE++ +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  
Sbjct: 310 GNEVDESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++
Sbjct: 490 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|256823391|ref|YP_003147354.1| RNA polymerase sigma-70 subunit RpoD [Kangiella koreensis DSM 16069]
 gi|256796930|gb|ACV27586.1| RNA polymerase, sigma 70 subunit, RpoD [Kangiella koreensis DSM
            16069]
          Length = 616

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 315/612 (51%), Positives = 421/612 (68%), Gaps = 20/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLT++E+ND LP DI+D E IE II+    M I V E   D + L++
Sbjct: 9    QLKLLIARGKEQGYLTYAEVNDHLPPDIVDPEQIEDIIRMINDMGIQVYETTPDADELLM 68

Query: 892  SNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            ++ + +D++  E   AAL++VDS+FGRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG
Sbjct: 69   NDESVTDEEAAEEAAAALASVDSEFGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEG 128

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            ++ ++ AI++ P TI  +L       + ++++ EIV G     FS         + +   
Sbjct: 129  IRQVLGAIANYPDTIRILLEEFALYQEEQVRLTEIVTG-----FSDGEEAEFVQEESEAA 183

Query: 1011 KILIESSSADLSTEQLEKLKY--------------ESLIKFSNISFHFDKMRKAFEKEGY 1056
            +I   +S    S +  +                  E+  +F+ +   +DK  KA +K G 
Sbjct: 184  QIAASASEELDSDDDADDDDDDEEETEVDTGPDPEEAAARFAELKKQYDKTVKAVDKYGR 243

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +S IK    +    + +R   +  + L   LR +++ + + E+ I+ + VN   MPR 
Sbjct: 244  THKSTIKQLEAMKELFMQLRLAPRMFDFLVTNLRQKMDGIREQERYIMMLSVNGARMPRK 303

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI  F  +E + +W++     +  Y+  L  +   I + Q+KL  ++    L + ++++
Sbjct: 304  TFISTFSGSETDPSWIEQHVTKKSKYSEPLAEHAEEILKAQRKLQIIEESCSLSVMEIKE 363

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
             NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364  ANREMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 424  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQP 483

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P DAA   S+
Sbjct: 484  EELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIDSPVDAATGESL 543

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            + V  +IL  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 544  KEVTDEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 603

Query: 1417 PSRYYKLKIFLE 1428
            PSR  KL+ +L+
Sbjct: 604  PSRSEKLRTYLD 615



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/599 (51%), Positives = 411/599 (68%), Gaps = 20/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLT++E+ND LP DI+D E IE II+    M I V E   D + L++
Sbjct: 9   QLKLLIARGKEQGYLTYAEVNDHLPPDIVDPEQIEDIIRMINDMGIQVYETTPDADELLM 68

Query: 102 SNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           ++ + +D++  E   AAL++VDS+FGRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG
Sbjct: 69  NDESVTDEEAAEEAAAALASVDSEFGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEG 128

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           ++ ++ AI++ P TI  +L       + ++++ EIV G     FS         + +   
Sbjct: 129 IRQVLGAIANYPDTIRILLEEFALYQEEQVRLTEIVTG-----FSDGEEAEFVQEESEAA 183

Query: 221 KILIESSSADLSTEQLEKLKY--------------ESLIKFSNISFHFDKMRKAFEKEGY 266
           +I   +S    S +  +                  E+  +F+ +   +DK  KA +K G 
Sbjct: 184 QIAASASEELDSDDDADDDDDDEEETEVDTGPDPEEAAARFAELKKQYDKTVKAVDKYGR 243

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +S IK    +    + +R   +  + L   LR +++ + + E+ I+ + VN   MPR 
Sbjct: 244 THKSTIKQLEAMKELFMQLRLAPRMFDFLVTNLRQKMDGIREQERYIMMLSVNGARMPRK 303

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI  F  +E + +W++     +  Y+  L  +   I + Q+KL  ++    L + ++++
Sbjct: 304 TFISTFSGSETDPSWIEQHVTKKSKYSEPLAEHAEEILKAQRKLQIIEESCSLSVMEIKE 363

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364 ANREMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 424 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQP 483

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P DAA   S+
Sbjct: 484 EELAERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIDSPVDAATGESL 543

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           + V  +IL  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 KEVTDEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|386824943|ref|ZP_10112071.1| RNA polymerase sigma factor RpoD [Serratia plymuthica PRI-2C]
 gi|386378110|gb|EIJ18919.1| RNA polymerase sigma factor RpoD [Serratia plymuthica PRI-2C]
          Length = 612

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 304/610 (49%), Positives = 421/610 (69%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E     ++   +   +  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182  HVGSELSTEEQNDDEEDEEDDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242  ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302  VTLFAGNETSDSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 542  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 601

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 602  RSEVLRSFLD 611



 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/597 (49%), Positives = 412/597 (69%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E     ++   +   +  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182 HVGSELSTEEQNDDEEDEEDDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242 ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302 VTLFAGNETSDSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|421785642|ref|ZP_16222067.1| RNA polymerase sigma factor [Serratia plymuthica A30]
 gi|407752257|gb|EKF62415.1| RNA polymerase sigma factor [Serratia plymuthica A30]
          Length = 612

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 305/610 (50%), Positives = 421/610 (69%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E     ++   +   E  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182  HVGSELSTEEQNDDEEDEDEDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242  ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302  VTLFAGNETSNSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 542  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 601

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 602  RSEVLRSFLD 611



 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 298/597 (49%), Positives = 412/597 (69%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E     ++   +   E  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182 HVGSELSTEEQNDDEEDEDEDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242 ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302 VTLFAGNETSNSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|254491243|ref|ZP_05104424.1| Sigma-70, non-essential region family [Methylophaga thiooxidans
            DMS010]
 gi|224463756|gb|EEF80024.1| Sigma-70, non-essential region family [Methylophaga thiooxydans
            DMS010]
          Length = 610

 Score =  595 bits (1533), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 309/609 (50%), Positives = 424/609 (69%), Gaps = 9/609 (1%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1    MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 886  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            T+ +  +   I+S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61   TDEMERLAEAISSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G I           K
Sbjct: 121  IAKRIEAGLRESLQMLSTYPDCIASFLELFDAVEAGEMRLNELIKGFIVAEEEVAEEEAK 180

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN---SE 1059
              + + EE         D S +  +  +    I        FD +R +F+   YN    +
Sbjct: 181  -EEVSVEESDSESDDDDDDSDDVSDDEEGSGEIDPEEAKARFDALRDSFK--AYNKAAGD 237

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            +  +A    SN  +  + T K++  L D + + I+++ + E+ I+ IVV++  M R  FI
Sbjct: 238  AAEEAREQTSNLFMEFKLTPKTLIYLNDLMADTIDEIRKQERTIMSIVVDQARMNRRDFI 297

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
              F  NE N+NW D   + +  Y+  + ++   +   Q KL  +  D  L ++++++I R
Sbjct: 298  DSFQGNESNVNWADKHIRAKKHYSSTIKKHHDEVVAAQSKLAEISEDRGLSISEIKEIAR 357

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+R
Sbjct: 358  QMSISEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 417

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP P  +
Sbjct: 418  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREPTPDEL 477

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++PSD+A+   +R  
Sbjct: 478  AERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISPSDSAIIEGLREA 537

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 538  TQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 597

Query: 1420 YYKLKIFLE 1428
              +L+ FL+
Sbjct: 598  SDQLRSFLD 606



 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 417/604 (69%), Gaps = 10/604 (1%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1   MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 96  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           T+ +  +   I+S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61  TDEMERLAEAISSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G I           K
Sbjct: 121 IAKRIEAGLRESLQMLSTYPDCIASFLELFDAVEAGEMRLNELIKGFIVAEEEVAEEEAK 180

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN---SE 269
             + + EE         D S +  +  +    I        FD +R +F+   YN    +
Sbjct: 181 -EEVSVEESDSESDDDDDDSDDVSDDEEGSGEIDPEEAKARFDALRDSFK--AYNKAAGD 237

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           +  +A    SN  +  + T K++  L D + + I+++ + E+ I+ IVV++  M R  FI
Sbjct: 238 AAEEAREQTSNLFMEFKLTPKTLIYLNDLMADTIDEIRKQERTIMSIVVDQARMNRRDFI 297

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
             F  NE N+NW D   + +  Y+  + ++   +   Q KL  +  D  L ++++++I R
Sbjct: 298 DSFQGNESNVNWADKHIRAKKHYSSTIKKHHDEVVAAQSKLAEISEDRGLSISEIKEIAR 357

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+R
Sbjct: 358 QMSISEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 417

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP P  +
Sbjct: 418 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREPTPDEL 477

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++PSD+A+   +R  
Sbjct: 478 AERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISPSDSAIIEGLREA 537

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLA 628
            + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P  
Sbjct: 538 TQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 597

Query: 629 HDWL 632
            D L
Sbjct: 598 SDQL 601


>gi|304396867|ref|ZP_07378747.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|440757198|ref|ZP_20936387.1| RNA polymerase sigma factor RpoD [Pantoea agglomerans 299R]
 gi|304355663|gb|EFM20030.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|436429025|gb|ELP26673.1| RNA polymerase sigma factor RpoD [Pantoea agglomerans 299R]
          Length = 613

 Score =  594 bits (1532), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 312/613 (50%), Positives = 423/613 (69%), Gaps = 14/613 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 997
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 998  --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
              + + + ++N++EE+   +  S+D       +L  E   KFS++   ++  R   + +G
Sbjct: 183  VGSELSEADRNDDEEEDEEDDDSSDDDNSIDPELARE---KFSDLRKQYEATRSVIKSKG 239

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+
Sbjct: 240  RSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPK 299

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 300  KNFITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVK 359

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 360  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 419

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 420  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 479

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 480  PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 539

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540  LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 600  HPSRSEVLRSFLD 612



 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 305/600 (50%), Positives = 414/600 (69%), Gaps = 14/600 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 207
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 208 --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
             + + + ++N++EE+   +  S+D       +L  E   KFS++   ++  R   + +G
Sbjct: 183 VGSELSEADRNDDEEEDEEDDDSSDDDNSIDPELARE---KFSDLRKQYEATRSVIKSKG 239

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+
Sbjct: 240 RSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPK 299

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 300 KNFITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVK 359

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 360 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 419

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 420 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 479

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 480 PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 539

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|271499150|ref|YP_003332175.1| RNA polymerase sigma-70 subunit RpoD [Dickeya dadantii Ech586]
 gi|270342705|gb|ACZ75470.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech586]
          Length = 611

 Score =  594 bits (1532), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/609 (51%), Positives = 416/609 (68%), Gaps = 8/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +        
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDLAPNAAPE 181

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 1059
            N E          D + E  +    ++ I       KF+ +   ++  R + +  G +  
Sbjct: 182  NAELADDGIDDDDDENEEDEDDTDDDNSIDPELARQKFTELRDQYEATRVSIKAHGRSHP 241

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            S I+  N +S      R   K  + L + +R+ +++V   E+QI+++ V  C MP+ +F+
Sbjct: 242  SAIEEINKLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRAQERQIMKLCVELCKMPKKNFV 301

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
             +F  NE N  W +    +   +   L      +    QKL  ++ +  L +  ++DINR
Sbjct: 302  TLFTGNETNSKWFEAAVSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINR 361

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 362  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 421

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 422  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 481

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 482  AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 541

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 542  THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 601

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 602  SEVLRSFLD 610



 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 305/596 (51%), Positives = 407/596 (68%), Gaps = 8/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +        
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDLAPNAAPE 181

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 269
           N E          D + E  +    ++ I       KF+ +   ++  R + +  G +  
Sbjct: 182 NAELADDGIDDDDDENEEDEDDTDDDNSIDPELARQKFTELRDQYEATRVSIKAHGRSHP 241

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           S I+  N +S      R   K  + L + +R+ +++V   E+QI+++ V  C MP+ +F+
Sbjct: 242 SAIEEINKLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRAQERQIMKLCVELCKMPKKNFV 301

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
            +F  NE N  W +    +   +   L      +    QKL  ++ +  L +  ++DINR
Sbjct: 302 TLFTGNETNSKWFEAAVSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINR 361

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 362 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 421

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 422 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 481

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 482 AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 541

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|429334653|ref|ZP_19215307.1| RNA polymerase sigma factor RpoD [Pseudomonas putida CSV86]
 gi|428760724|gb|EKX82984.1| RNA polymerase sigma factor RpoD [Pseudomonas putida CSV86]
          Length = 616

 Score =  594 bits (1532), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/614 (50%), Positives = 419/614 (68%), Gaps = 25/614 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID + S             E  
Sbjct: 130  REVMSAIAHFPGTVEYILGEYDRVTAEGGRLSDVLSGYIDPDDSI--------AAPAEMP 181

Query: 1012 ILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFHFDKMRKAFEKE 1054
              +++ +A  +    E  + +                    +F  ++   +   K  +K 
Sbjct: 182  PPVDTKAAPAADSDDEDEEKDESGDEEEETESGPDPEVARQRFGAVAEQLEATAKILKKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +S+  +     ++   + I+   K  E L + +R  ++++   E+ I+++ V    MP
Sbjct: 242  GRDSKQGVAELLALAELFMPIKLVPKQFEVLVERVRGALDRLRAQERAIMQLCVRDARMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R  F+++FP NE++L W  +  K    +   L R    I   QQKL++L+ +  L + ++
Sbjct: 302  RADFLRLFPSNEVDLTWSGDLAKRSTKWAEALGRLDADIVRCQQKLVDLEAETGLTIAEI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   
Sbjct: 482  TPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVE 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHP+R   L+ FL+
Sbjct: 602  RHPTRSEHLRSFLD 615



 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 304/601 (50%), Positives = 410/601 (68%), Gaps = 25/601 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID + S             E  
Sbjct: 130 REVMSAIAHFPGTVEYILGEYDRVTAEGGRLSDVLSGYIDPDDSI--------AAPAEMP 181

Query: 222 ILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFHFDKMRKAFEKE 264
             +++ +A  +    E  + +                    +F  ++   +   K  +K 
Sbjct: 182 PPVDTKAAPAADSDDEDEEKDESGDEEEETESGPDPEVARQRFGAVAEQLEATAKILKKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +S+  +     ++   + I+   K  E L + +R  ++++   E+ I+++ V    MP
Sbjct: 242 GRDSKQGVAELLALAELFMPIKLVPKQFEVLVERVRGALDRLRAQERAIMQLCVRDARMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R  F+++FP NE++L W  +  K    +   L R    I   QQKL++L+ +  L + ++
Sbjct: 302 RADFLRLFPSNEVDLTWSGDLAKRSTKWAEALGRLDADIVRCQQKLVDLEAETGLTIAEI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   
Sbjct: 482 TPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVE 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S++   +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|345871733|ref|ZP_08823676.1| RNA polymerase, sigma 70 subunit, RpoD [Thiorhodococcus drewsii AZ1]
 gi|343920119|gb|EGV30858.1| RNA polymerase, sigma 70 subunit, RpoD [Thiorhodococcus drewsii AZ1]
          Length = 619

 Score =  594 bits (1531), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/619 (50%), Positives = 416/619 (67%), Gaps = 40/619 (6%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 894
            LI  GKE+GYLT++E+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13   LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVDQTLSDSA 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73   VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELTIAKRIEDGLTQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            + A+S  P +I +++   D++ + E ++ +++ G               N    E +  +
Sbjct: 133  LTALSVYPRSIEKLIEIFDRVEREETRLTDVISGF--------------NDLEEEPETPV 178

Query: 1015 ESSSADLSTEQLEKLKY-------------------------ESLIKFSNISFHFDKMRK 1049
             SS A  S    +  +                          E+  + + +   F+ +R 
Sbjct: 179  PSSPAAASVHSDKSDEDTDGDEDSDDDDDDDAAVVDTGPDPEEAARRAALLRDGFEVLRV 238

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            + E+ G + E    A   +S   L  +  A   ++L + LR  I ++   E+ I+ + V+
Sbjct: 239  SLEQHGRDDERSRAAMAAVSEIFLQFKLVAPVFQELAEILRGTIERIRSQERLIMSMCVD 298

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            + GMPR  FI+ FP NE N  W+D      H Y   L  N   I+  Q+KL  ++ +  L
Sbjct: 299  QAGMPRKQFIETFPRNETNSEWLDQLLASGHSYATRLEENASEIRRAQRKLQEVERENYL 358

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             + +++++NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359  TIGEIKEVNRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE
Sbjct: 419  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQE 478

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G E  P  +A +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D
Sbjct: 479  MGREATPEELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVD 538

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A    +R   +++L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 539  SATAEGLREATQNMLSSLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 598

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHP+R  KL+ FL+
Sbjct: 599  ALRKLRHPTRSDKLRSFLD 617



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/614 (50%), Positives = 409/614 (66%), Gaps = 41/614 (6%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 104
           LI  GKE+GYLT++E+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13  LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVDQTLSDSA 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            SDD+  EA  AAL+TVDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIE+GL  +
Sbjct: 73  VSDDEAAEAAAAALATVDSEFGRTTDPVRMYMREMGTVELLTREGELTIAKRIEDGLTQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           + A+S  P +I +++   D++ + E ++ +++ G               N    E +  +
Sbjct: 133 LTALSVYPRSIEKLIEIFDRVEREETRLTDVISGF--------------NDLEEEPETPV 178

Query: 225 ESSSADLSTEQLEKLKY-------------------------ESLIKFSNISFHFDKMRK 259
            SS A  S    +  +                          E+  + + +   F+ +R 
Sbjct: 179 PSSPAAASVHSDKSDEDTDGDEDSDDDDDDDAAVVDTGPDPEEAARRAALLRDGFEVLRV 238

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
           + E+ G + E    A   +S   L  +  A   ++L + LR  I ++   E+ I+ + V+
Sbjct: 239 SLEQHGRDDERSRAAMAAVSEIFLQFKLVAPVFQELAEILRGTIERIRSQERLIMSMCVD 298

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           + GMPR  FI+ FP NE N  W+D      H Y   L  N   I+  Q+KL  ++ +  L
Sbjct: 299 QAGMPRKQFIETFPRNETNSEWLDQLLASGHSYATRLEENASEIRRAQRKLQEVERENYL 358

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            + +++++NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359 TIGEIKEVNRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE
Sbjct: 419 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQE 478

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G E  P  +A +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D
Sbjct: 479 MGREATPEELAERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPVD 538

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A    +R   +++L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 539 SATAEGLREATQNMLSSLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 598

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 599 ALRKLRHPTRSDKL 612


>gi|420375358|ref|ZP_14875229.1| RNA polymerase sigma factor rpoD [Shigella flexneri 1235-66]
 gi|391312754|gb|EIQ70361.1| RNA polymerase sigma factor rpoD [Shigella flexneri 1235-66]
          Length = 614

 Score =  594 bits (1531), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   +  +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEDDDDSSDDDNSIDPELAREKFGELRTQYEITRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   +  +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEDDDDSSDDDNSIDPELAREKFGELRTQYEITRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|398844525|ref|ZP_10601587.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM84]
 gi|398254462|gb|EJN39557.1| RNA polymerase sigma factor, sigma-70 family [Pseudomonas sp. GM84]
          Length = 616

 Score =  593 bits (1530), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/606 (51%), Positives = 424/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++   +   ++ S++  E+ +       +  +F  +S       K  +K G +    I
Sbjct: 190  AAKEESDDEEESEESSDDEEEAESGPDPVVAAQRFGAVSDQLAVTLKVLKKHGRSHAESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   +++  + I+   K  + L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  GAMQALADLFMPIKLVPKQFDVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  580 bits (1494), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 306/593 (51%), Positives = 415/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVTTEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++   +   ++ S++  E+ +       +  +F  +S       K  +K G +    I
Sbjct: 190 AAKEESDDEEESEESSDDEEEAESGPDPVVAAQRFGAVSDQLAVTLKVLKKHGRSHAESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   +++  + I+   K  + L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 GAMQALADLFMPIKLVPKQFDVLVERVRDALSRLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|157148639|ref|YP_001455958.1| RNA polymerase sigma factor RpoD [Citrobacter koseri ATCC BAA-895]
 gi|157085844|gb|ABV15522.1| hypothetical protein CKO_04466 [Citrobacter koseri ATCC BAA-895]
          Length = 614

 Score =  593 bits (1530), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 304/611 (49%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
              +   +  ++    +   E  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183  VGSELSQEEMDDDDDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 1065 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            H +   E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HADAQTEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/598 (49%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
             +   +  ++    +   E  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183 VGSELSQEEMDDDDDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 275 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           H +   E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HADAQTEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|308188146|ref|YP_003932277.1| RNA polymerase sigma factor rpoD (sigma-70) [Pantoea vagans C9-1]
 gi|308058656|gb|ADO10828.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pantoea vagans C9-1]
          Length = 613

 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/613 (50%), Positives = 423/613 (69%), Gaps = 14/613 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 997
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 998  --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
              + + + ++N+++E+   +  S+D       +L  E   KFS++   ++  R   + +G
Sbjct: 183  VGSELSEADRNDDDEEDEEDDDSSDDDNSIDPELARE---KFSDLRKQYETTRDVIKSKG 239

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+
Sbjct: 240  RSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPK 299

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 300  KNFITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVK 359

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 360  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 419

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 420  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 479

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 480  PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 539

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540  LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 600  HPSRSEVLRSFLD 612



 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 304/600 (50%), Positives = 414/600 (69%), Gaps = 14/600 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 207
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 208 --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
             + + + ++N+++E+   +  S+D       +L  E   KFS++   ++  R   + +G
Sbjct: 183 VGSELSEADRNDDDEEDEEDDDSSDDDNSIDPELARE---KFSDLRKQYETTRDVIKSKG 239

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+
Sbjct: 240 RSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPK 299

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 300 KNFITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVK 359

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 360 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 419

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 420 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 479

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 480 PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 539

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|336247240|ref|YP_004590950.1| RNA polymerase sigma factor RpoD [Enterobacter aerogenes KCTC 2190]
 gi|444354644|ref|YP_007390788.1| RNA polymerase sigma factor RpoD [Enterobacter aerogenes EA1509E]
 gi|334733296|gb|AEG95671.1| RNA polymerase sigma factor RpoD [Enterobacter aerogenes KCTC 2190]
 gi|443905474|emb|CCG33248.1| RNA polymerase sigma factor RpoD [Enterobacter aerogenes EA1509E]
          Length = 614

 Score =  593 bits (1529), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 419/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   +  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEEEDDDDDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAVAMNKPWSEKLHDVKEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 410/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   +  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEEEDDDDDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAVAMNKPWSEKLHDVKEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|307129360|ref|YP_003881376.1| RNA polymerase sigma-70 (sigma D) factor [Dickeya dadantii 3937]
 gi|306526889|gb|ADM96819.1| RNA polymerase, sigma 70 (sigma D) factor [Dickeya dadantii 3937]
          Length = 611

 Score =  593 bits (1528), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/611 (50%), Positives = 419/611 (68%), Gaps = 12/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--------SSNN 998
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N         +  N
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPSTTPEN 182

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
              + G+  +++++   +          ++ +L  +   KF+ +   ++  R + +  G +
Sbjct: 183  AELAGDGMDDDDENEEDEEDDTDDDNSIDPELARQ---KFTELRDQYEATRVSIKAHGRS 239

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              + I   N +S      R   K  + L + +R  +++V   E+QI+++ V  C MP+ +
Sbjct: 240  HPTAIDEINKLSEVFKQFRLVPKQFDLLVNNMRAMMDRVRAQERQIMKLCVELCKMPKKN 299

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+ +F  NE N  W D    +   +   L      +    QKL  ++ +  L +  ++DI
Sbjct: 300  FVTLFTGNETNRKWFDAALSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDI 359

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 420  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 479

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 480  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 539

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 540  SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 599

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 600  SRSEVLRSFLD 610



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 303/598 (50%), Positives = 410/598 (68%), Gaps = 12/598 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--------SSNN 208
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N         +  N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPSTTPEN 182

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
             + G+  +++++   +          ++ +L  +   KF+ +   ++  R + +  G +
Sbjct: 183 AELAGDGMDDDDENEEDEEDDTDDDNSIDPELARQ---KFTELRDQYEATRVSIKAHGRS 239

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             + I   N +S      R   K  + L + +R  +++V   E+QI+++ V  C MP+ +
Sbjct: 240 HPTAIDEINKLSEVFKQFRLVPKQFDLLVNNMRAMMDRVRAQERQIMKLCVELCKMPKKN 299

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+ +F  NE N  W D    +   +   L      +    QKL  ++ +  L +  ++DI
Sbjct: 300 FVTLFTGNETNRKWFDAALSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDI 359

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 420 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 479

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 480 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 539

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|377579556|ref|ZP_09808522.1| RNA polymerase sigma-D factor [Escherichia hermannii NBRC 105704]
 gi|377539093|dbj|GAB53687.1| RNA polymerase sigma-D factor [Escherichia hermannii NBRC 105704]
          Length = 614

 Score =  593 bits (1528), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 304/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +      +E    +   E  +    ++ I       KFS +   ++  R   + +G +
Sbjct: 183  VGSELSSEELEDDDDEDEDEDDDSSDDDNTIDPELAREKFSELRVQYEAARVVIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             ++  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  DKAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFTAALAMNKPWSEKLKDVAEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +      +E    +   E  +    ++ I       KFS +   ++  R   + +G +
Sbjct: 183 VGSELSSEELEDDDDEDEDEDDDSSDDDNTIDPELAREKFSELRVQYEAARVVIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            ++  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 DKAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFTAALAMNKPWSEKLKDVAEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|251791058|ref|YP_003005779.1| RNA polymerase sigma factor RpoD [Dickeya zeae Ech1591]
 gi|247539679|gb|ACT08300.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya zeae Ech1591]
          Length = 611

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/608 (50%), Positives = 416/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       +N
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPNVAPEN 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 1060
                   I+    +   ++ +     S+       KF+ +   ++  R + +  G +  S
Sbjct: 183  AELADDGIDDDDDENEEDEDDTDDDNSIDPELARQKFTELRDQYEATRVSIKAHGRSHPS 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I+  N +S      R   K  + L + +R+ +++V   E+QI+++ V  C MP+ +F+ 
Sbjct: 243  AIEEINKLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRTQERQIMKLCVELCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N  W +    +   +   L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFTGNETNSKWFEAALSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 303/595 (50%), Positives = 407/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       +N
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPNVAPEN 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 270
                  I+    +   ++ +     S+       KF+ +   ++  R + +  G +  S
Sbjct: 183 AELADDGIDDDDDENEEDEDDTDDDNSIDPELARQKFTELRDQYEATRVSIKAHGRSHPS 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I+  N +S      R   K  + L + +R+ +++V   E+QI+++ V  C MP+ +F+ 
Sbjct: 243 AIEEINKLSEVFKQFRLVPKQFDLLVNNMRSMMDRVRTQERQIMKLCVELCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N  W +    +   +   L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFTGNETNSKWFEAALSMGKPWCEKLREVEDDVHRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|389680928|ref|ZP_10172274.1| RNA polymerase sigma factor RpoD [Pseudomonas chlororaphis O6]
 gi|388555217|gb|EIM18464.1| RNA polymerase sigma factor RpoD [Pseudomonas chlororaphis O6]
          Length = 602

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 309/601 (51%), Positives = 419/601 (69%), Gaps = 8/601 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            +I  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L+   
Sbjct: 1    MISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAEAD 60

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 61   TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 120

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 1010
             AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 121  GAIAHFPGTVEHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKAAKAD 180

Query: 1011 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  +     
Sbjct: 181  DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGREHKQALAEMLA 240

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 241  LAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 300

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 301  DESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 360

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 361  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 420

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 421  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 480

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 481  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 540

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 541  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEHLRSFL 600

Query: 1428 E 1428
            +
Sbjct: 601  D 601



 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 303/588 (51%), Positives = 410/588 (69%), Gaps = 8/588 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           +I  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L+   
Sbjct: 1   MISRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLLAEAD 60

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 61  TDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 120

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNEE 220
            AI+  P T+  IL    +++    ++ +++ G ID +      ++        K    +
Sbjct: 121 GAIAHFPGTVEHILSEYTRVTTEGGRLSDVLSGYIDPDDGIAPPAAEVPPPVDAKAAKAD 180

Query: 221 KILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  +     E+  +   + +I   +F  ++   +  RKA +K G   +  +     
Sbjct: 181 DDTDDDDAEASDDEEEAESGPDPVIAAQRFGAVADQMEITRKALKKHGREHKQALAEMLA 240

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++   + I+   K  E L + +R+ ++++ Q E+ I+++ V    MPR  F++ FP NE+
Sbjct: 241 LAELFMPIKLVPKQFEGLVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRQFPGNEV 300

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           + +W D   K +  Y   + R  P I   QQKL  L+T+  L + +++DINR+M  GE K
Sbjct: 301 DESWSDALAKGKAKYAEAIGRLQPDIIRCQQKLTALETETGLTIAEIKDINRRMSIGEAK 360

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 361 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 420

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 421 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 480

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L+ L
Sbjct: 481 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVLSGL 540

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 588


>gi|375124995|ref|ZP_09770159.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Gallinarum str. SG9]
 gi|326629245|gb|EGE35588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Gallinarum str. SG9]
          Length = 660

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/655 (47%), Positives = 431/655 (65%), Gaps = 18/655 (2%)

Query: 792  DKYDPDSYIR----KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKER 843
            D+  PDS       K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 244

Query: 1022 STEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
              +  +    +        +  KF+ +   +   R   + +G +  +  +    +S    
Sbjct: 245  EEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFK 304

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +
Sbjct: 305  QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+
Sbjct: 365  AAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 424

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 425  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 484

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK+
Sbjct: 485  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 544

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+K
Sbjct: 545  LKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 604

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/637 (47%), Positives = 421/637 (66%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMR
Sbjct: 550 EPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMR 609

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>gi|56415151|ref|YP_152226.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Paratyphi A str. ATCC 9150]
 gi|197364081|ref|YP_002143718.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Paratyphi A str. AKU_12601]
 gi|205358509|ref|ZP_02656872.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Kentucky str. CDC 191]
 gi|205359720|ref|ZP_02831723.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Weltevreden str. HI_N05-537]
 gi|375003048|ref|ZP_09727388.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Infantis str. SARB27]
 gi|375120701|ref|ZP_09765868.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. SD3246]
 gi|378446562|ref|YP_005234194.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. D23580]
 gi|378452027|ref|YP_005239387.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. 14028S]
 gi|378990530|ref|YP_005253694.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. UK-1]
 gi|379702473|ref|YP_005244201.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. ST4/74]
 gi|409246931|ref|YP_006887633.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica subsp.
            enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|421883914|ref|ZP_16315136.1| RNA polymerase sigma factor rpoD [Salmonella enterica subsp. enterica
            serovar Senftenberg str. SS209]
 gi|16421768|gb|AAL22085.1| sigma D factor of RNA polymerase [Salmonella enterica subsp. enterica
            serovar Typhimurium str. LT2]
 gi|56129408|gb|AAV78914.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Paratyphi A str. ATCC 9150]
 gi|197095558|emb|CAR61123.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Paratyphi A str. AKU_12601]
 gi|205333914|gb|EDZ20678.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Kentucky str. CDC 191]
 gi|205343355|gb|EDZ30119.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Weltevreden str. HI_N05-537]
 gi|261248341|emb|CBG26178.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. D23580]
 gi|267995406|gb|ACY90291.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. 14028S]
 gi|320087665|emb|CBY97429.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica subsp.
            enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|323131572|gb|ADX19002.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. ST4/74]
 gi|326624968|gb|EGE31313.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. SD3246]
 gi|332990077|gb|AEF09060.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. UK-1]
 gi|353077736|gb|EHB43496.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Infantis str. SARB27]
 gi|379986515|emb|CCF87409.1| RNA polymerase sigma factor rpoD [Salmonella enterica subsp. enterica
            serovar Senftenberg str. SS209]
          Length = 660

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/655 (47%), Positives = 431/655 (65%), Gaps = 18/655 (2%)

Query: 792  DKYDPDSYIR----KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKER 843
            D+  PDS       K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 244

Query: 1022 STEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
              +  +    +        +  KF+ +   +   R   + +G +  +  +    +S    
Sbjct: 245  EEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFK 304

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +
Sbjct: 305  QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+
Sbjct: 365  AAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 424

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 425  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 484

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK+
Sbjct: 485  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 544

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+K
Sbjct: 545  LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 604

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/637 (47%), Positives = 421/637 (66%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMR
Sbjct: 550 EPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMR 609

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>gi|114321663|ref|YP_743346.1| RNA polymerase sigma-70 subunit RpoD [Alkalilimnicola ehrlichii
            MLHE-1]
 gi|114228057|gb|ABI57856.1| RNA polymerase, sigma 70 subunit, RpoD [Alkalilimnicola ehrlichii
            MLHE-1]
          Length = 598

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/606 (51%), Positives = 428/606 (70%), Gaps = 15/606 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            ++ + + K LI  GKE+G+LT++E+ND LP+DI+D E IE II     M I+V E   D 
Sbjct: 3    QDQQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGINVHEVAPDA 62

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+LS+  +++D+D  E   AAL+ VD++FGRT DP++MYMREMG+VELLTR+GEIE+A
Sbjct: 63   DELLLSDAAVSTDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGTVELLTREGEIELA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIK 1002
            KRIEEGL  ++ A+S+ P    ++L    K+   E++++E++ G    D+  S+ +    
Sbjct: 123  KRIEEGLDQVLAALSAYPGAAAKLLDLYRKVQDGEMRLNELMGGFRNPDEELSAYSADAG 182

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++ + E+ ++++        +L          F  ++    +M++   ++G +S    
Sbjct: 183  KEEDEDGEEAVVDNGPDPEMAAEL----------FRRLAEADQRMQEVLRRQGSDSPECA 232

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            +    ++   L  +F  K I++L D LR  +N + + E+ IL+    K GMPR  F++ F
Sbjct: 233  ELREQLAEIFLTFKFPPKIIDQLVDGLRRDVNVLRRNERHILK-ACTKAGMPRKTFVRSF 291

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
               E +  W+D     +  +   L  +   I+  QQ LI+ +  + + + +++DINR+M 
Sbjct: 292  ISRETDPGWLDEMLASKEPWAQRLAEHEDDIRRAQQVLIDAERKVGMTIGEIKDINRRMS 351

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 352  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +
Sbjct: 412  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPDELAER 471

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N ++P D+A    +R  VK 
Sbjct: 472  MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDINAMSPVDSATREGLRESVKG 531

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 532  VLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEG 591

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 592  LRSFLD 597



 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 305/593 (51%), Positives = 419/593 (70%), Gaps = 15/593 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           ++ + + K LI  GKE+G+LT++E+ND LP+DI+D E IE II     M I+V E   D 
Sbjct: 3   QDQQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPEQIEDIIGMINDMGINVHEVAPDA 62

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+LS+  +++D+D  E   AAL+ VD++FGRT DP++MYMREMG+VELLTR+GEIE+A
Sbjct: 63  DELLLSDAAVSTDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGTVELLTREGEIELA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIK 212
           KRIEEGL  ++ A+S+ P    ++L    K+   E++++E++ G    D+  S+ +    
Sbjct: 123 KRIEEGLDQVLAALSAYPGAAAKLLDLYRKVQDGEMRLNELMGGFRNPDEELSAYSADAG 182

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++ + E+ ++++        +L          F  ++    +M++   ++G +S    
Sbjct: 183 KEEDEDGEEAVVDNGPDPEMAAEL----------FRRLAEADQRMQEVLRRQGSDSPECA 232

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           +    ++   L  +F  K I++L D LR  +N + + E+ IL+    K GMPR  F++ F
Sbjct: 233 ELREQLAEIFLTFKFPPKIIDQLVDGLRRDVNVLRRNERHILK-ACTKAGMPRKTFVRSF 291

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
              E +  W+D     +  +   L  +   I+  QQ LI+ +  + + + +++DINR+M 
Sbjct: 292 ISRETDPGWLDEMLASKEPWAQRLAEHEDDIRRAQQVLIDAERKVGMTIGEIKDINRRMS 351

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 352 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +
Sbjct: 412 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPDELAER 471

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N ++P D+A    +R  VK 
Sbjct: 472 MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDINAMSPVDSATREGLRESVKG 531

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 532 VLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|386828955|ref|ZP_10116062.1| RNA polymerase sigma factor, sigma-70 family [Beggiatoa alba B18LD]
 gi|386429839|gb|EIJ43667.1| RNA polymerase sigma factor, sigma-70 family [Beggiatoa alba B18LD]
          Length = 620

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 316/612 (51%), Positives = 424/612 (69%), Gaps = 15/612 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV-SEHVLDTETLM 890
            + K+LI  GKE+G+LT+ E+ND LP+D++D E IE +I     M I V  E+V D ++L+
Sbjct: 9    QLKLLIAKGKEQGFLTYHEVNDHLPDDLVDPEQIEGVISMINDMGIMVHDEYVPDADSLL 68

Query: 891  LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +S+      D+D  E   AAL++VDS+FGRT DP++MYMREMG+V+LLTR+GEI+IAKRI
Sbjct: 69   MSDNAVAPDDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVDLLTREGEIKIAKRI 128

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            EEGL   + A+++ P  I E L   DK++  E+K+ +++ G  D     +         N
Sbjct: 129  EEGLTQALTALATHPDIIGEFLSLFDKVASEEVKLSDLISGFADHTNPDDEVPAAALSEN 188

Query: 1008 NEE----KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA-------FEKEGY 1056
             EE    +++  S S     ++   +  E  +     S  F ++R+A        +K G 
Sbjct: 189  AEEMDEDEMMTVSGSTGGDDDEEGGMLEEVTLDMEEASNRFARLREAHQQMVTMLDKHGL 248

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS  + +A  ++++  L  +   K I+ L   L+N +  + + E  I +I + K  M + 
Sbjct: 249  NSPEFQQARQDVTDVFLQFKLVTKLIDDLSLRLQNDVATIREQENVIRDICIKKVLMDKK 308

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+  F  N  N +W+ N  K    Y   L ++   + + Q KLI ++    L L ++++
Sbjct: 309  EFLSSFKNNMTNPDWIPNLLKGNKAYVENLKKHAEDLIQHQSKLIAMEKQSRLDLAEIKE 368

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 369  INRRMSIGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 428

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            Y+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQILQE G E  P
Sbjct: 429  YKRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQILQEKGREATP 488

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A KMEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++ AP ++A    +
Sbjct: 489  EELAEKMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSIPAPLESATFEGL 548

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R   +++L+SLTPRE+KVLRMRFGI+MS+DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 549  RRATQEMLHSLTPREAKVLRMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 608

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 609  PSRSEQLRSFLD 620



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/599 (51%), Positives = 414/599 (69%), Gaps = 15/599 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV-SEHVLDTETLM 100
           + K+LI  GKE+G+LT+ E+ND LP+D++D E IE +I     M I V  E+V D ++L+
Sbjct: 9   QLKLLIAKGKEQGFLTYHEVNDHLPDDLVDPEQIEGVISMINDMGIMVHDEYVPDADSLL 68

Query: 101 LSN---ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +S+      D+D  E   AAL++VDS+FGRT DP++MYMREMG+V+LLTR+GEI+IAKRI
Sbjct: 69  MSDNAVAPDDEDAAEEAAAALASVDSEFGRTTDPVRMYMREMGTVDLLTREGEIKIAKRI 128

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           EEGL   + A+++ P  I E L   DK++  E+K+ +++ G  D     +         N
Sbjct: 129 EEGLTQALTALATHPDIIGEFLSLFDKVASEEVKLSDLISGFADHTNPDDEVPAAALSEN 188

Query: 218 NEE----KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA-------FEKEGY 266
            EE    +++  S S     ++   +  E  +     S  F ++R+A        +K G 
Sbjct: 189 AEEMDEDEMMTVSGSTGGDDDEEGGMLEEVTLDMEEASNRFARLREAHQQMVTMLDKHGL 248

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS  + +A  ++++  L  +   K I+ L   L+N +  + + E  I +I + K  M + 
Sbjct: 249 NSPEFQQARQDVTDVFLQFKLVTKLIDDLSLRLQNDVATIREQENVIRDICIKKVLMDKK 308

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+  F  N  N +W+ N  K    Y   L ++   + + Q KLI ++    L L ++++
Sbjct: 309 EFLSSFKNNMTNPDWIPNLLKGNKAYVENLKKHAEDLIQHQSKLIAMEKQSRLDLAEIKE 368

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 369 INRRMSIGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 428

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           Y+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQILQE G E  P
Sbjct: 429 YKRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQILQEKGREATP 488

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A KMEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++ AP ++A    +
Sbjct: 489 EELAEKMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSIPAPLESATFEGL 548

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R   +++L+SLTPRE+KVLRMRFGI+MS+DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 RRATQEMLHSLTPREAKVLRMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 607


>gi|372275337|ref|ZP_09511373.1| RNA polymerase sigma factor RpoD [Pantoea sp. SL1_M5]
          Length = 613

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/619 (50%), Positives = 417/619 (67%), Gaps = 26/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 993
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 S  +R     ++  ++    + +S D       +L  E   KFS++   ++  R 
Sbjct: 183  VGSELSDADRKDDEEEDEEDDDSSDDDNSID------PELARE---KFSDLRKQYETTRA 233

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              + +G +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ + 
Sbjct: 234  VIKSKGRSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIE 293

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
             C MP+ +FI +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 294  LCKMPKKNFITLFTGNETNETWFKAALAMNKPWSEKLLEVQDDVTRSLQKLAQVEEETGL 353

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 354  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 413

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 414  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 473

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 474  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 533

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 534  SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 593

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 594  ALRKLRHPSRSEVLRSFLD 612



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/606 (50%), Positives = 408/606 (67%), Gaps = 26/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 203
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                S  +R     ++  ++    + +S D       +L  E   KFS++   ++  R 
Sbjct: 183 VGSELSDADRKDDEEEDEEDDDSSDDDNSID------PELARE---KFSDLRKQYETTRA 233

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             + +G +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ + 
Sbjct: 234 VIKSKGRSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIE 293

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
            C MP+ +FI +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 294 LCKMPKKNFITLFTGNETNETWFKAALAMNKPWSEKLLEVQDDVTRSLQKLAQVEEETGL 353

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 354 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 413

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 414 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 473

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 474 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 533

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 534 SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 593

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 594 ALRKLR 599


>gi|334125660|ref|ZP_08499649.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterobacter
            hormaechei ATCC 49162]
 gi|333387123|gb|EGK58327.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterobacter
            hormaechei ATCC 49162]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|295097580|emb|CBK86670.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae subsp.
            cloacae NCTC 9394]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 419/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E+ +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEEDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 410/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E+ +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEEDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|440232604|ref|YP_007346397.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia marcescens FGI94]
 gi|440054309|gb|AGB84212.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia marcescens FGI94]
          Length = 634

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 307/616 (49%), Positives = 422/616 (68%), Gaps = 21/616 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 84

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 85   DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 144

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 1000
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 145  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 204

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 1059
            I    +  E+    +    D  +E    +  E +  KF+ +   ++  R+  +  G    
Sbjct: 205  IGSELSTEEQDDDDDEDDEDDDSEDDNSIDPEVARQKFTELREQYEATRQVIKANG---- 260

Query: 1060 SYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
               ++H   + E+L +       R   K  + L +++R  +++V   E+ I+++ V +C 
Sbjct: 261  ---RSHAKSAEEILKLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKMCVEQCK 317

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MP+ +F+ +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L + 
Sbjct: 318  MPKKNFVTLFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTIE 377

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 378  QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 437

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 438  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 497

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A 
Sbjct: 498  EPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSAT 557

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 558  SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 617

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FL+
Sbjct: 618  KLRHPSRSEVLRSFLD 633



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/603 (49%), Positives = 413/603 (68%), Gaps = 21/603 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 84

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 85  DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 144

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 210
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 145 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 204

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 269
           I    +  E+    +    D  +E    +  E +  KF+ +   ++  R+  +  G    
Sbjct: 205 IGSELSTEEQDDDDDEDDEDDDSEDDNSIDPEVARQKFTELREQYEATRQVIKANG---- 260

Query: 270 SYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
              ++H   + E+L +       R   K  + L +++R  +++V   E+ I+++ V +C 
Sbjct: 261 ---RSHAKSAEEILKLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERIIMKMCVEQCK 317

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MP+ +F+ +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L + 
Sbjct: 318 MPKKNFVTLFAGNETSDSWFEAALAMAKPWSEKLKDVAEDVQRSLQKLRQIEEETGLTIE 377

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
            ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 378 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 437

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 438 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 497

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A 
Sbjct: 498 EPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSAT 557

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 558 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 617

Query: 623 KLR 625
           KLR
Sbjct: 618 KLR 620


>gi|429101731|ref|ZP_19163705.1| RNA polymerase sigma factor RpoD [Cronobacter turicensis 564]
 gi|426288380|emb|CCJ89818.1| RNA polymerase sigma factor RpoD [Cronobacter turicensis 564]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|390435428|ref|ZP_10223966.1| RNA polymerase sigma factor RpoD [Pantoea agglomerans IG1]
          Length = 613

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/619 (50%), Positives = 417/619 (67%), Gaps = 26/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 993
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 S  +R     ++  ++    + +S D       +L  E   KFS++   ++  R 
Sbjct: 183  VGSELSEADRKDDEEEDEEDDDSSDDDNSID------PELARE---KFSDLRKQYETTRA 233

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              + +G +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ + 
Sbjct: 234  VIKSKGRSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIE 293

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
             C MP+ +FI +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 294  LCKMPKKNFITLFTGNETNETWFKAALAMNKPWSEKLLEVQDDVTRSLQKLAQVEEETGL 353

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 354  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 413

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 414  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 473

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 474  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 533

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 534  SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 593

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 594  ALRKLRHPSRSEVLRSFLD 612



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/606 (50%), Positives = 408/606 (67%), Gaps = 26/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 203
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                S  +R     ++  ++    + +S D       +L  E   KFS++   ++  R 
Sbjct: 183 VGSELSEADRKDDEEEDEEDDDSSDDDNSID------PELARE---KFSDLRKQYETTRA 233

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             + +G +  + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ + 
Sbjct: 234 VIKSKGRSHAAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIE 293

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
            C MP+ +FI +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 294 LCKMPKKNFITLFTGNETNETWFKAALAMNKPWSEKLLEVQDDVTRSLQKLAQVEEETGL 353

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 354 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 413

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 414 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 473

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 474 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 533

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 534 SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 593

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 594 ALRKLR 599


>gi|381402875|ref|ZP_09927559.1| RNA polymerase sigma factor RpoD [Pantoea sp. Sc1]
 gi|380736074|gb|EIB97137.1| RNA polymerase sigma factor RpoD [Pantoea sp. Sc1]
          Length = 613

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 308/610 (50%), Positives = 416/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNS 1058
             G++ +  ++   E    D      +    +  +   KFS++   ++  R   + +G + 
Sbjct: 183  VGSELSEADRNDDEDEDEDEDDNSEDDNSIDPELAREKFSDLRKQYETTRSVIKSKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243  AAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 301/597 (50%), Positives = 407/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNS 268
            G++ +  ++   E    D      +    +  +   KFS++   ++  R   + +G + 
Sbjct: 183 VGSELSEADRNDDEDEDEDEDDNSEDDNSIDPELAREKFSDLRKQYETTRSVIKSKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            + +    N+S+     R   K  + L  ++R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243 AAAVAEIQNLSDVFKQFRLVPKQFDYLVGSMRTMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETNESWFKAALAMNKPWSEKLLEVQDDVMRSLQKLAQVEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|291618943|ref|YP_003521685.1| RpoD [Pantoea ananatis LMG 20103]
 gi|378765638|ref|YP_005194098.1| RNA polymerase sigma factor RpoD [Pantoea ananatis LMG 5342]
 gi|386017213|ref|YP_005935511.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
 gi|386077919|ref|YP_005991444.1| RNA polymerase sigma factor RpoD [Pantoea ananatis PA13]
 gi|291153973|gb|ADD78557.1| RpoD [Pantoea ananatis LMG 20103]
 gi|327395293|dbj|BAK12715.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
 gi|354987100|gb|AER31224.1| RNA polymerase sigma factor RpoD [Pantoea ananatis PA13]
 gi|365185111|emb|CCF08061.1| RNA polymerase sigma factor RpoD [Pantoea ananatis LMG 5342]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 308/614 (50%), Positives = 421/614 (68%), Gaps = 15/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 997
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 998  --NRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKE 1054
              + + + ++N++E+        +      ++ +L  E   KFS++   ++  R   + +
Sbjct: 183  VGSELSEADRNDDEDDDEESDDDSSDDDNSIDPELARE---KFSDLRTQYETTRDVIKSK 239

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +  + +    N+S+     R   K  + L + +R  + +V   E+ I+++ +  C MP
Sbjct: 240  GRSHAASVAEIQNLSDVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMP 299

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            + +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  +
Sbjct: 300  KKNFITLFTGNETNESWFKAALAMNKPWSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQV 359

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 360  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 419

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 420  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 479

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 480  TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 539

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 540  SLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 599

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 600  RHPSRSEVLRSFLD 613



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 301/601 (50%), Positives = 412/601 (68%), Gaps = 15/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 207
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 208 --NRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKE 264
             + + + ++N++E+        +      ++ +L  E   KFS++   ++  R   + +
Sbjct: 183 VGSELSEADRNDDEDDDEESDDDSSDDDNSIDPELARE---KFSDLRTQYETTRDVIKSK 239

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +  + +    N+S+     R   K  + L + +R  + +V   E+ I+++ +  C MP
Sbjct: 240 GRSHAASVAEIQNLSDVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMP 299

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           + +FI +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  +
Sbjct: 300 KKNFITLFTGNETNESWFKAALAMNKPWSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQV 359

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 360 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 419

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 420 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 479

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 480 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 539

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 540 SLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 599

Query: 625 R 625
           R
Sbjct: 600 R 600


>gi|419959930|ref|ZP_14475978.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp. cloacae
            GS1]
 gi|388605210|gb|EIM34432.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp. cloacae
            GS1]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 417/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R     +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIRAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 408/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R     +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIRAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLHQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|156932573|ref|YP_001436489.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ATCC BAA-894]
 gi|389839627|ref|YP_006341711.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ES15]
 gi|417789808|ref|ZP_12437416.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii E899]
 gi|424801030|ref|ZP_18226572.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii 696]
 gi|429106160|ref|ZP_19168029.1| RNA polymerase sigma factor RpoD [Cronobacter malonaticus 681]
 gi|429111584|ref|ZP_19173354.1| RNA polymerase sigma factor RpoD [Cronobacter malonaticus 507]
 gi|449306897|ref|YP_007439253.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii SP291]
 gi|156530827|gb|ABU75653.1| hypothetical protein ESA_00355 [Cronobacter sakazakii ATCC BAA-894]
 gi|333956007|gb|EGL73702.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii E899]
 gi|387850103|gb|AFJ98200.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ES15]
 gi|423236751|emb|CCK08442.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii 696]
 gi|426292883|emb|CCJ94142.1| RNA polymerase sigma factor RpoD [Cronobacter malonaticus 681]
 gi|426312741|emb|CCJ99467.1| RNA polymerase sigma factor RpoD [Cronobacter malonaticus 507]
 gi|449096930|gb|AGE84964.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii SP291]
          Length = 614

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|146313109|ref|YP_001178183.1| RNA polymerase sigma factor RpoD [Enterobacter sp. 638]
 gi|145319985|gb|ABP62132.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter sp. 638]
          Length = 631

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 307/611 (50%), Positives = 420/611 (68%), Gaps = 11/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 22   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 81

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 82   DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +I+ G +D N  +   V    
Sbjct: 142  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIITGFVDPN--AEEEVAPTA 199

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
             +   E    E    +   E+ E+ + ++ I       KF  +   ++  R   + +G +
Sbjct: 200  THVGSELTKEEREENEEEDEEDEEEEDDNSIDPELAREKFGELRTQYELARDTIKAKGRS 259

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S+     R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 260  HAAAKEEIQKLSDVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 319

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 320  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVSDDVQRGLQKLRQIEEETGLTIEQVKDI 379

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 380  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 439

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 440  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 499

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 500  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 559

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 560  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 619

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 620  SRSEVLRSFLD 630



 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/598 (50%), Positives = 411/598 (68%), Gaps = 11/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 22  QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 81

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 82  DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +I+ G +D N  +   V    
Sbjct: 142 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIITGFVDPN--AEEEVAPTA 199

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
            +   E    E    +   E+ E+ + ++ I       KF  +   ++  R   + +G +
Sbjct: 200 THVGSELTKEEREENEEEDEEDEEEEDDNSIDPELAREKFGELRTQYELARDTIKAKGRS 259

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S+     R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 260 HAAAKEEIQKLSDVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 319

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 320 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVSDDVQRGLQKLRQIEEETGLTIEQVKDI 379

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 380 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 439

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 440 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 499

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 500 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 559

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 560 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 617


>gi|389783156|ref|ZP_10194650.1| RNA polymerase sigma factor RpoD [Rhodanobacter spathiphylli B39]
 gi|388435094|gb|EIL92012.1| RNA polymerase sigma factor RpoD [Rhodanobacter spathiphylli B39]
          Length = 626

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 318/623 (51%), Positives = 415/623 (66%), Gaps = 36/623 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL-- 889
            + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+T+  
Sbjct: 12   EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDTISD 71

Query: 890  --MLSNITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
                   T DDD   EEA  A LS VD++ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 72   GAAPGGGTGDDDSAAEEAV-ALLSAVDAEVGRTTDPVRMYMREMGTVELLTREGEIAIAK 130

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEGL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       +
Sbjct: 131  RIEEGLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAADL-----AR 185

Query: 1006 NNNEEKILIESS-------------------SADLSTEQLEKLKYESLIKFSNISFHFDK 1046
               E   L+                       A  S    E++K     +   +  ++ K
Sbjct: 186  KEKEAAALLAPEVEEGEEGDEDEDESSEDEEEAGPSGPDPEEVKR----RMELLRDYYGK 241

Query: 1047 MRKAFEKEG-YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
             +KA  K      +  +K  + ++ E L ++  +  I+     LR  +  +   E+ +L+
Sbjct: 242  FQKAAPKAASITDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVGDIRHHERVLLD 301

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            I V +  MP+  FIK FP NE NL W     + +  ++  +  +  +I   Q+KL  ++ 
Sbjct: 302  IFVKQVKMPKAEFIKTFPSNEGNLEWAAELGRKRQKWSPNIKTHREAIDAEQEKLAAIER 361

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             + LPL D++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 362  KLFLPLIDIKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 421

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 422  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 481

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQ+ G E  P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  
Sbjct: 482  MLQQFGREATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNAS 541

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P D+A    +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 542  SPIDSATETGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 601

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR  +L+ FL+
Sbjct: 602  IEAKALRKLRHPSRSEQLRSFLD 624



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/610 (50%), Positives = 405/610 (66%), Gaps = 36/610 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL-- 99
           + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+T+  
Sbjct: 12  EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDTISD 71

Query: 100 --MLSNITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
                  T DDD   EEA  A LS VD++ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 72  GAAPGGGTGDDDSAAEEAV-ALLSAVDAEVGRTTDPVRMYMREMGTVELLTREGEIAIAK 130

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEGL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       +
Sbjct: 131 RIEEGLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAADL-----AR 185

Query: 216 NNNEEKILIESS-------------------SADLSTEQLEKLKYESLIKFSNISFHFDK 256
              E   L+                       A  S    E++K     +   +  ++ K
Sbjct: 186 KEKEAAALLAPEVEEGEEGDEDEDESSEDEEEAGPSGPDPEEVKR----RMELLRDYYGK 241

Query: 257 MRKAFEKEG-YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
            +KA  K      +  +K  + ++ E L ++  +  I+     LR  +  +   E+ +L+
Sbjct: 242 FQKAAPKAASITDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVGDIRHHERVLLD 301

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           I V +  MP+  FIK FP NE NL W     + +  ++  +  +  +I   Q+KL  ++ 
Sbjct: 302 IFVKQVKMPKAEFIKTFPSNEGNLEWAAELGRKRQKWSPNIKTHREAIDAEQEKLAAIER 361

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            + LPL D++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 362 KLFLPLIDIKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 421

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 422 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 481

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQ+ G E  P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  
Sbjct: 482 MLQQFGREATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNAS 541

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P D+A    +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 542 SPIDSATETGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 601

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 602 IEAKALRKLR 611


>gi|340000732|ref|YP_004731616.1| RNA polymerase sigma-70 factor [Salmonella bongori NCTC 12419]
 gi|339514094|emb|CCC31857.1| RNA polymerase sigma-70 factor [Salmonella bongori NCTC 12419]
          Length = 660

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/655 (47%), Positives = 431/655 (65%), Gaps = 18/655 (2%)

Query: 792  DKYDPDSYI--RKFGYKIFSKKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKER 843
            D+  PDS    ++  YK     N  S+ + +N   +       +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVGSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 244

Query: 1022 STEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
              +  +    +        +  KF+ +   +   R   + +G +  +  +    +S    
Sbjct: 245  EEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFK 304

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +
Sbjct: 305  QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+
Sbjct: 365  AAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 424

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 425  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 484

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK+
Sbjct: 485  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 544

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+K
Sbjct: 545  LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 604

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/637 (47%), Positives = 421/637 (66%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVGSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMR
Sbjct: 550 EPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMR 609

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>gi|344342690|ref|ZP_08773561.1| RNA polymerase, sigma 70 subunit, RpoD [Marichromatium purpuratum
            984]
 gi|343806026|gb|EGV23921.1| RNA polymerase, sigma 70 subunit, RpoD [Marichromatium purpuratum
            984]
          Length = 621

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/622 (50%), Positives = 420/622 (67%), Gaps = 24/622 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ + + K LI  GKE+G+LT++E+ND LP  I++ E IE I++    M I V E   D+
Sbjct: 4    EHHQSQLKQLIARGKEQGFLTYAEVNDHLPPGIVEAEQIEDIVRMINDMGIMVHETAPDS 63

Query: 887  ETLMLSN-ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            +   LS+   SDD+  EA  AAL++VDS+FGRT DP++MYMREMGSVELLTR+GE+ IAK
Sbjct: 64   DDQTLSDSAVSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGSVELLTREGELIIAK 123

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNN 998
            RIE+GL  ++ A+S  P  +  ++   D++ + E ++ +++ G  D              
Sbjct: 124  RIEDGLNQVLAALSVYPRAVERLIELFDQVEREEKRLTDVISGFNDATDDEPATPVQHGQ 183

Query: 999  RVIKGNKNNNEEKILIES-----------SSADLSTEQLEKLKYESLIKFSNISFHFDKM 1047
               + +KNN       +            +  D   +  +  +   L++      HF  M
Sbjct: 184  SAQQKDKNNAAADDDADHGDADDDDDEDDTPVDTGPDPEDAARRAKLLRE-----HFAVM 238

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            R+A E+ G + E   KA    S   L  +  A   ++L + LR  I ++   E+QI  + 
Sbjct: 239  REALEQYGRDDERSRKAMAETSEVFLEFKLVAAVFQELAELLRGTIERIRAQERQIQSLC 298

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V + G+PR  FI+ F  NE +  W+D        Y   L      ++  Q+KL +L+ + 
Sbjct: 299  VRQAGVPRKAFIEGFSGNESSPEWLDKLLASGKPYAARLEPLAVDVRRAQRKLQDLEREN 358

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + +++D+NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 359  FLTITEVKDVNRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 418

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++
Sbjct: 419  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMI 478

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G E  P  +AI+M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P
Sbjct: 479  QEMGREATPEELAIRMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAGVVSP 538

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A +  +R   +++L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 539  VDSATSEGLREATQNMLASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 598

Query: 1408 AKALRKLRHPSRYYKLKIFLEG 1429
            AKALRKLRHP+R  +L+ FL+ 
Sbjct: 599  AKALRKLRHPTRSERLRSFLDA 620



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 306/608 (50%), Positives = 410/608 (67%), Gaps = 24/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ + + K LI  GKE+G+LT++E+ND LP  I++ E IE I++    M I V E   D+
Sbjct: 4   EHHQSQLKQLIARGKEQGFLTYAEVNDHLPPGIVEAEQIEDIVRMINDMGIMVHETAPDS 63

Query: 97  ETLMLSN-ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           +   LS+   SDD+  EA  AAL++VDS+FGRT DP++MYMREMGSVELLTR+GE+ IAK
Sbjct: 64  DDQTLSDSAVSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGSVELLTREGELIIAK 123

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNN 208
           RIE+GL  ++ A+S  P  +  ++   D++ + E ++ +++ G  D              
Sbjct: 124 RIEDGLNQVLAALSVYPRAVERLIELFDQVEREEKRLTDVISGFNDATDDEPATPVQHGQ 183

Query: 209 RVIKGNKNNNEEKILIES-----------SSADLSTEQLEKLKYESLIKFSNISFHFDKM 257
              + +KNN       +            +  D   +  +  +   L++      HF  M
Sbjct: 184 SAQQKDKNNAAADDDADHGDADDDDDEDDTPVDTGPDPEDAARRAKLLRE-----HFAVM 238

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           R+A E+ G + E   KA    S   L  +  A   ++L + LR  I ++   E+QI  + 
Sbjct: 239 REALEQYGRDDERSRKAMAETSEVFLEFKLVAAVFQELAELLRGTIERIRAQERQIQSLC 298

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V + G+PR  FI+ F  NE +  W+D        Y   L      ++  Q+KL +L+ + 
Sbjct: 299 VRQAGVPRKAFIEGFSGNESSPEWLDKLLASGKPYAARLEPLAVDVRRAQRKLQDLEREN 358

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + +++D+NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 359 FLTITEVKDVNRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 418

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++
Sbjct: 419 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMI 478

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G E  P  +AI+M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P
Sbjct: 479 QEMGREATPEELAIRMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDAGVVSP 538

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A +  +R   +++L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 539 VDSATSEGLREATQNMLASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 598

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 599 AKALRKLR 606


>gi|283787203|ref|YP_003367068.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
 gi|282950657|emb|CBG90329.1| RNA polymerase sigma-70 factor [Citrobacter rodentium ICC168]
          Length = 614

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
              +   +  ++    +   E  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183  VGSELSQEDLDDDEDEDEEEDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 1065 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            H +   E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HADAQAEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADEVHRGLQKLHQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
             +   +  ++    +   E  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183 VGSELSQEDLDDDEDEDEEEDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 275 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           H +   E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HADAQAEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADEVHRGLQKLHQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|423122213|ref|ZP_17109897.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5246]
 gi|376392842|gb|EHT05504.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5246]
          Length = 614

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   +  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEDDDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L  ++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVGSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   +  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEDDDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L  ++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVGSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVQRGLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|283836397|ref|ZP_06356138.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
 gi|291067770|gb|EFE05879.1| RNA polymerase sigma factor RpoD [Citrobacter youngae ATCC 29220]
          Length = 615

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 300/612 (49%), Positives = 416/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183  VGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFAELRTQYEITRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 293/599 (48%), Positives = 407/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183 VGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFAELRTQYEITRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|384227506|ref|YP_005619251.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Ak
            (Acyrthosiphon kondoi)]
 gi|345538446|gb|AEO08423.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Ak
            (Acyrthosiphon kondoi)]
          Length = 612

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 320/619 (51%), Positives = 428/619 (69%), Gaps = 27/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLITHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS---SNNRV 1000
            AKRIEEG+  +  ++S  P  I  +L   D++   ++++ +I+ G +D N     S + +
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQMRLSDIITGFVDPNAEEIFSPSAI 181

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
              G++  +EE+     S+ +   +  E  + +  I     +  F ++R  +       ++
Sbjct: 182  HIGSELLDEEQ-----SNDEDEEDNQEDHEDDHSIDPELANEKFAELRVQYNNTNNTIKN 236

Query: 1061 YIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
              + H        N+S      R   K  + L + +R+ + +V   E+ I+++ V  C M
Sbjct: 237  KNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRDMMERVRTEERIIIKLCVEICKM 296

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVL 1169
            P+ +FIKVFP  +IN  W   E     + N     N+  +KE      +KLI ++ +  L
Sbjct: 297  PKKNFIKVFPVKKINNFWFIKE----QNTNQPWSENLKKVKEDVFISIKKLIKIEEETGL 352

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 353  TIEQVKDINKRMSIGESKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 412

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 413  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 472

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D
Sbjct: 473  IGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLD 532

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 533  SATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 592

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 593  ALRKLRHPSRSEVLRSFLD 611



 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 313/606 (51%), Positives = 419/606 (69%), Gaps = 27/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLITHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS---SNNRV 210
           AKRIEEG+  +  ++S  P  I  +L   D++   ++++ +I+ G +D N     S + +
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQMRLSDIITGFVDPNAEEIFSPSAI 181

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
             G++  +EE+     S+ +   +  E  + +  I     +  F ++R  +       ++
Sbjct: 182 HIGSELLDEEQ-----SNDEDEEDNQEDHEDDHSIDPELANEKFAELRVQYNNTNNTIKN 236

Query: 271 YIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
             + H        N+S      R   K  + L + +R+ + +V   E+ I+++ V  C M
Sbjct: 237 KNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRDMMERVRTEERIIIKLCVEICKM 296

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVL 379
           P+ +FIKVFP  +IN  W   E     + N     N+  +KE      +KLI ++ +  L
Sbjct: 297 PKKNFIKVFPVKKINNFWFIKE----QNTNQPWSENLKKVKEDVFISIKKLIKIEEETGL 352

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 353 TIEQVKDINKRMSIGESKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 412

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 413 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 472

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D
Sbjct: 473 IGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLD 532

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 533 SATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 592

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 593 ALRKLR 598


>gi|16761985|ref|NP_457602.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. CT18]
 gi|25288442|pir||AB0893 RNA polymerase sigma-70 factor [imported] - Salmonella enterica
            subsp. enterica serovar Typhi (strain CT18)
 gi|16504288|emb|CAD07736.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhi]
 gi|29139106|gb|AAO70674.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhi str. Ty2]
          Length = 660

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 308/641 (48%), Positives = 426/641 (66%), Gaps = 14/641 (2%)

Query: 802  KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPE 857
            K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+GYLT++E+ND LPE
Sbjct: 19   KYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPE 78

Query: 858  DIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEAALSTVDSDF 915
            DI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA    LS+V+S+ 
Sbjct: 79   DIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQVLSSVESEI 138

Query: 916  GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI 975
            GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I  +L   D++
Sbjct: 139  GRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRV 198

Query: 976  SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--- 1032
               E ++ +++ G +D N          +  +   +  ++    +   +  +    +   
Sbjct: 199  EAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGDDDAADDDNS 258

Query: 1033 -----SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 1087
                 +  KF+ +   +   R   + +G +  +  +    +S      R   K  + L +
Sbjct: 259  IDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVN 318

Query: 1088 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILC 1147
            ++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +   ++  L 
Sbjct: 319  SMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKLH 378

Query: 1148 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 1207
                 ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIA
Sbjct: 379  DVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIA 438

Query: 1208 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 1267
            KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR
Sbjct: 439  KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 498

Query: 1268 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327
            IPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+
Sbjct: 499  IPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI 558

Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387
            GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DH
Sbjct: 559  GDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDH 618

Query: 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 619  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/637 (47%), Positives = 421/637 (66%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMR
Sbjct: 550 EPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMR 609

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>gi|1575485|gb|AAB09543.1| LprpoD [Legionella pneumophila]
          Length = 620

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 320/607 (52%), Positives = 421/607 (69%), Gaps = 18/607 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 1012
            + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134  LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 1013 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
            L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194  LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
            ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314  TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             G+ +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  IGD-EARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 431  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 490

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 491  MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 550

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  K
Sbjct: 551  ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEK 610

Query: 1423 LKIFLEG 1429
            L+ FLEG
Sbjct: 611  LRSFLEG 617



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 310/593 (52%), Positives = 410/593 (69%), Gaps = 18/593 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    + E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPSEDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL--IDKNFSSNNRVIKGNKNNNEEKI 222
           + +++  P T+  +L   D+    EI+++EI+ G   +D+  +    +        +E+I
Sbjct: 134 LKSLAHYPETVQLVLEDYDRFLAEEIRLNEIISGFADVDEEIAPATNIGSMLDEEQQEEI 193

Query: 223 LIE------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
           L++           +S         ++ I F  +   F+K  KA ++ G  ++  ++  +
Sbjct: 194 LLDVDEEDEDGEGGISDVDDGPNPEQAKIYFDELREAFEKAMKALKEHGRTNKKTVELLD 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
           ++S   L ++ T++ ++KL    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 SMSESFLKLKLTSRQVDKLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKI-QHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            +L W+  ET I +H   L L R   N   I  LQ KL + + +  L +++++DINRKM 
Sbjct: 314 TDLGWL--ETIISKHAKKLDLQRIEENREEILRLQSKLASFEIEYGLTISEIKDINRKMS 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            G+ +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 IGD-EARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A K
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEK 490

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           ME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +
Sbjct: 491 MELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLE 550

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 ILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|407801337|ref|ZP_11148181.1| RNA polymerase sigma factor RpoD [Alcanivorax sp. W11-5]
 gi|407024774|gb|EKE36517.1| RNA polymerase sigma factor RpoD [Alcanivorax sp. W11-5]
          Length = 626

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 305/637 (47%), Positives = 428/637 (67%), Gaps = 52/637 (8%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI LGK++GYLT++E+ND LP+ I D + +E II+    M I V E   D 
Sbjct: 6    EQQQSQLKQLIALGKDQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGIPVVEKASDA 65

Query: 887  ETLMLS-NITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + LM+  N  S D+V  A EAA  L++V S+ GRT DP++MYMREMG+VELLTR+GEIEI
Sbjct: 66   DQLMMDENADSTDEVA-AEEAAGVLASVGSEPGRTTDPVRMYMREMGTVELLTREGEIEI 124

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+++++HA++  P ++  +L   DKI+  E +I +++ G +D N          
Sbjct: 125  AKRIEEGIREVLHAMAYWPGSVEVVLGEFDKITTEERRISDLIAGYLDPN---------- 174

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFS 1038
               ++      + + A  +  + EK K                              +F+
Sbjct: 175  ---DDGAAAPSQPTEAQFAARKEEKAKAAEGDEEEDDDSDDDSDEDDGSIDPVLAAERFN 231

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 1098
             +   ++K++++ ++ G +  +  K    ++      +   +  ++L   +RN ++ + +
Sbjct: 232  ELRARWEKVQRSLKRNGRDHATTGKQLEQMAEMFTLFKLVPRVYDELLRQVRNTLDVIRR 291

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-----ETKIQHD-YNLILCRNIPS 1152
             E++++ + + + GM R  FIK FP NE N+ W D+     + K+  D +N++       
Sbjct: 292  HEREVMALAIKRGGMDRKDFIKTFPGNETNVEWADDMLRNKKVKLDQDRFNVVK----DD 347

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I   Q++++ +     LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 348  ILRTQKRILQISEAAGLPVADIKEINRRVSIGEAKARRAKKEMVEANLRLVISIAKKYTN 407

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 408  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 467

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINKI+R+ RQ+LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDED
Sbjct: 468  IETINKINRVQRQMLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDED 527

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            S LGDFIED N+ +P D+A    +    +++L +LT RE+KVLRMRFGI+M++DHTLEEV
Sbjct: 528  SSLGDFIEDANIESPVDSATMLGLEEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEV 587

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+G
Sbjct: 588  GKQFDVTRERIRQIEAKALRKLRHPSRSEHLRSFLDG 624



 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/623 (47%), Positives = 418/623 (67%), Gaps = 52/623 (8%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI LGK++GYLT++E+ND LP+ I D + +E II+    M I V E   D 
Sbjct: 6   EQQQSQLKQLIALGKDQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGIPVVEKASDA 65

Query: 97  ETLMLS-NITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + LM+  N  S D+V  A EAA  L++V S+ GRT DP++MYMREMG+VELLTR+GEIEI
Sbjct: 66  DQLMMDENADSTDEVA-AEEAAGVLASVGSEPGRTTDPVRMYMREMGTVELLTREGEIEI 124

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+++++HA++  P ++  +L   DKI+  E +I +++ G +D N          
Sbjct: 125 AKRIEEGIREVLHAMAYWPGSVEVVLGEFDKITTEERRISDLIAGYLDPN---------- 174

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFS 248
              ++      + + A  +  + EK K                              +F+
Sbjct: 175 ---DDGAAAPSQPTEAQFAARKEEKAKAAEGDEEEDDDSDDDSDEDDGSIDPVLAAERFN 231

Query: 249 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQ 308
            +   ++K++++ ++ G +  +  K    ++      +   +  ++L   +RN ++ + +
Sbjct: 232 ELRARWEKVQRSLKRNGRDHATTGKQLEQMAEMFTLFKLVPRVYDELLRQVRNTLDVIRR 291

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-----ETKIQHD-YNLILCRNIPS 362
            E++++ + + + GM R  FIK FP NE N+ W D+     + K+  D +N++       
Sbjct: 292 HEREVMALAIKRGGMDRKDFIKTFPGNETNVEWADDMLRNKKVKLDQDRFNVVK----DD 347

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I   Q++++ +     LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 348 ILRTQKRILQISEAAGLPVADIKEINRRVSIGEAKARRAKKEMVEANLRLVISIAKKYTN 407

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 408 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 467

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINKI+R+ RQ+LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDED
Sbjct: 468 IETINKINRVQRQMLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDED 527

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           S LGDFIED N+ +P D+A    +    +++L +LT RE+KVLRMRFGI+M++DHTLEEV
Sbjct: 528 SSLGDFIEDANIESPVDSATMLGLEEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEV 587

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 588 GKQFDVTRERIRQIEAKALRKLR 610


>gi|375257437|ref|YP_005016607.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca KCTC 1686]
 gi|397660046|ref|YP_006500748.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca E718]
 gi|423110410|ref|ZP_17098105.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5243]
 gi|423116425|ref|ZP_17104116.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5245]
 gi|365906915|gb|AEX02368.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca KCTC 1686]
 gi|376378607|gb|EHS91366.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5245]
 gi|376379569|gb|EHS92321.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5243]
 gi|394348132|gb|AFN34253.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca E718]
          Length = 614

 Score =  591 bits (1524), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 417/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 408/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|197286218|ref|YP_002152090.1| RNA polymerase sigma factor RpoD [Proteus mirabilis HI4320]
 gi|227357334|ref|ZP_03841691.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
 gi|425069984|ref|ZP_18473099.1| RNA polymerase sigma factor rpoD [Proteus mirabilis WGLW6]
 gi|425071354|ref|ZP_18474460.1| RNA polymerase sigma factor rpoD [Proteus mirabilis WGLW4]
 gi|194683705|emb|CAR44685.1| RNA polymerase sigma-70 factor [Proteus mirabilis HI4320]
 gi|227162597|gb|EEI47586.1| RNA polymerase sigma-70 factor [Proteus mirabilis ATCC 29906]
 gi|404596171|gb|EKA96696.1| RNA polymerase sigma factor rpoD [Proteus mirabilis WGLW6]
 gi|404599161|gb|EKA99621.1| RNA polymerase sigma factor rpoD [Proteus mirabilis WGLW4]
          Length = 618

 Score =  591 bits (1524), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/622 (49%), Positives = 418/622 (67%), Gaps = 27/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENSNDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++   ID N          N
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITAFIDPNAEEVAESDDVN 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEK 1053
               ++++I   +   D   ++      +S             KF+ +   ++K R++ + 
Sbjct: 183  LGKDDDEIDNSADDEDEDEDEDSDTDSDSDDDNSIDPELARQKFTELREQYEKTRQSIKA 242

Query: 1054 EGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            +G N       H +   E+L +       R   K  + L + +R  +++V   E+ I+ +
Sbjct: 243  KGRN-------HKDTELEILQLSEIFKQFRLVPKQFDYLVNNMREMMDRVRAQERHIMRL 295

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V++  MP+ +FI +F  NE N  W      +   ++  L      ++   QKL  ++ +
Sbjct: 296  CVDQVKMPKKNFITLFTGNETNDTWFTAARAMNKPWSEKLAGIEEEVQRSLQKLQQIEVE 355

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 356  TGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 415

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 416  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 475

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 476  LQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 535

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 536  PLDSATSESLRSATHEVLGGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 595

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 596  EAKALRKLRHPSRSEVLRSFLD 617



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/609 (49%), Positives = 409/609 (67%), Gaps = 27/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENSNDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++   ID N          N
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITAFIDPNAEEVAESDDVN 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEK 263
              ++++I   +   D   ++      +S             KF+ +   ++K R++ + 
Sbjct: 183 LGKDDDEIDNSADDEDEDEDEDSDTDSDSDDDNSIDPELARQKFTELREQYEKTRQSIKA 242

Query: 264 EGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           +G N       H +   E+L +       R   K  + L + +R  +++V   E+ I+ +
Sbjct: 243 KGRN-------HKDTELEILQLSEIFKQFRLVPKQFDYLVNNMREMMDRVRAQERHIMRL 295

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V++  MP+ +FI +F  NE N  W      +   ++  L      ++   QKL  ++ +
Sbjct: 296 CVDQVKMPKKNFITLFTGNETNDTWFTAARAMNKPWSEKLAGIEEEVQRSLQKLQQIEVE 355

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 356 TGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 415

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 416 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 475

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 476 LQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 535

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 536 PLDSATSESLRSATHEVLGGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 595

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 596 EAKALRKLR 604


>gi|365103141|ref|ZP_09333173.1| RNA polymerase sigma factor rpoD [Citrobacter freundii 4_7_47CFAA]
 gi|395228345|ref|ZP_10406668.1| RNA polymerase sigma factor rpoD [Citrobacter sp. A1]
 gi|421845166|ref|ZP_16278321.1| RNA polymerase sigma factor RpoD [Citrobacter freundii ATCC 8090 =
            MTCC 1658]
 gi|424732034|ref|ZP_18160615.1| rna polymerase sigma factor rpod [Citrobacter sp. L17]
 gi|363645480|gb|EHL84743.1| RNA polymerase sigma factor rpoD [Citrobacter freundii 4_7_47CFAA]
 gi|394717994|gb|EJF23638.1| RNA polymerase sigma factor rpoD [Citrobacter sp. A1]
 gi|411773487|gb|EKS57032.1| RNA polymerase sigma factor RpoD [Citrobacter freundii ATCC 8090 =
            MTCC 1658]
 gi|422893662|gb|EKU33509.1| rna polymerase sigma factor rpod [Citrobacter sp. L17]
 gi|455642706|gb|EMF21857.1| RNA polymerase sigma factor RpoD [Citrobacter freundii GTC 09479]
          Length = 615

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 300/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF  +   ++  R   + +G 
Sbjct: 183  VGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFGELRTQYEITRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 293/599 (48%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF  +   ++  R   + +G 
Sbjct: 183 VGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFGELRTQYEITRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|261342495|ref|ZP_05970353.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
            35316]
 gi|288315137|gb|EFC54075.1| RNA polymerase sigma factor RpoD [Enterobacter cancerogenus ATCC
            35316]
          Length = 614

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 305/621 (49%), Positives = 419/621 (67%), Gaps = 29/621 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELARDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEQILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ + 
Sbjct: 303  FITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKDDVHRGLQKLQQIEEET 352

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353  GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473  QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533  LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 593  AKALRKLRHPSRSEVLRSFLD 613



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 298/608 (49%), Positives = 410/608 (67%), Gaps = 29/608 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELARDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEQILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ + 
Sbjct: 303 FITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKDDVHRGLQKLQQIEEET 352

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353 GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473 QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533 LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 593 AKALRKLR 600


>gi|288941560|ref|YP_003443800.1| RNA polymerase sigma-70 subunit RpoD [Allochromatium vinosum DSM 180]
 gi|288896932|gb|ADC62768.1| RNA polymerase, sigma 70 subunit, RpoD [Allochromatium vinosum DSM
            180]
          Length = 623

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 305/611 (49%), Positives = 422/611 (69%), Gaps = 20/611 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 894
            LI  GKE+GYLT++E+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13   LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVDHTLSDSA 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             SDD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE++IAKRIE+GL  +
Sbjct: 73   VSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRIEDGLNQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            ++A+S  P +I +++   D++ + E ++ +++ G  D+   ++  +    +  +E     
Sbjct: 133  LNALSVYPRSIEKLIEIFDRVDREEARLTDVISGFNDEATETDETLATDVQAASETDA-- 190

Query: 1015 ESSSADLSTEQLEKLKY----------------ESLIKFSNI-SFHFDKMRKAFEKEGYN 1057
            ++   DL  E  +                    E   + +N+    +  ++ A E+ G +
Sbjct: 191  DADKTDLDVEAADLDSDDDDDSATVEVDTGPDPEDAARRANLLRERYQTLKAALEEYGRD 250

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             E   +A   +S   L  +  +   ++L + LR  I ++   E+ I+ + V + GM R  
Sbjct: 251  DERSREAMQAVSEVFLQFKLVSPVFQELAEILRATIERIRAQERAIMSLCVEQAGMGRKE 310

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ FP NE N  W+D        +++ L    P I+  Q+KL +++ + +L + +++++
Sbjct: 311  FIETFPSNETNPEWLDGLIARGRPFSVRLQELAPDIQRAQRKLQDIERENILTIGEIKEV 370

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 371  NRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 430

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P 
Sbjct: 431  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPE 490

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R
Sbjct: 491  ELAARMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPLDSATAEGLR 550

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 551  EATQNMLASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 610

Query: 1418 SRYYKLKIFLE 1428
            +R  KL+ FL+
Sbjct: 611  TRSDKLRSFLD 621



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 301/606 (49%), Positives = 415/606 (68%), Gaps = 21/606 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 104
           LI  GKE+GYLT++E+ND LP  I++ + IE I++    M I V E   D     LS+  
Sbjct: 13  LIAKGKEQGYLTYTEVNDHLPPGIVETDQIEDIVRMINDMGIMVQETAPDVVDHTLSDSA 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            SDD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE++IAKRIE+GL  +
Sbjct: 73  VSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRIEDGLNQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           ++A+S  P +I +++   D++ + E ++ +++ G  D+   ++  +    +  +E     
Sbjct: 133 LNALSVYPRSIEKLIEIFDRVDREEARLTDVISGFNDEATETDETLATDVQAASETDA-- 190

Query: 225 ESSSADLSTEQLEKLKY----------------ESLIKFSNI-SFHFDKMRKAFEKEGYN 267
           ++   DL  E  +                    E   + +N+    +  ++ A E+ G +
Sbjct: 191 DADKTDLDVEAADLDSDDDDDSATVEVDTGPDPEDAARRANLLRERYQTLKAALEEYGRD 250

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            E   +A   +S   L  +  +   ++L + LR  I ++   E+ I+ + V + GM R  
Sbjct: 251 DERSREAMQAVSEVFLQFKLVSPVFQELAEILRATIERIRAQERAIMSLCVEQAGMGRKE 310

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ FP NE N  W+D        +++ L    P I+  Q+KL +++ + +L + +++++
Sbjct: 311 FIETFPSNETNPEWLDGLIARGRPFSVRLQELAPDIQRAQRKLQDIERENILTIGEIKEV 370

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NRKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 371 NRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 430

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P 
Sbjct: 431 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPE 490

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R
Sbjct: 491 ELAARMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSGVISPLDSATAEGLR 550

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-P 626
              +++L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P
Sbjct: 551 EATQNMLASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 610

Query: 627 LAHDWL 632
              D L
Sbjct: 611 TRSDKL 616


>gi|317493716|ref|ZP_07952133.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
            9_2_54FAA]
 gi|365834774|ref|ZP_09376213.1| RNA polymerase sigma factor RpoD [Hafnia alvei ATCC 51873]
 gi|316918043|gb|EFV39385.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
            9_2_54FAA]
 gi|364567855|gb|EHM45504.1| RNA polymerase sigma factor RpoD [Hafnia alvei ATCC 51873]
          Length = 610

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/607 (51%), Positives = 417/607 (68%), Gaps = 5/607 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVIKG 1003
            IE+G+  +  +++  P  I  +L   D++   E ++ +I+ G +D N   +        G
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIITGFVDPNAEEDLAPTATNVG 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESY 1061
            ++ ++E+    +    +    + +      L   KFS +   ++K R A +  G +    
Sbjct: 183  SELSSEDLNDDDEEEDEDDDSEDDNSIDPELARQKFSELREQYEKTRVAIKTHGRSHAKA 242

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +   N+S      R   K  + L + +R  +++V   E+ I+++ V +  MP+ +FI +
Sbjct: 243  AEEILNLSEVFKQFRLVPKQFDYLVNNMRQMMDRVRTQERLIMKLCVEQSKMPKKNFITL 302

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE N  W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+M
Sbjct: 303  FTGNETNTTWFDAALAMAKPWGEKLKDVREDVERSLQKLHQIEEETGLTIEQVKDINRRM 362

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 363  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 422

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 423  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAE 482

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  +
Sbjct: 483  RMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATR 542

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 543  DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 602

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 603  VLRSFLD 609



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 303/594 (51%), Positives = 408/594 (68%), Gaps = 5/594 (0%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVIKG 213
           IE+G+  +  +++  P  I  +L   D++   E ++ +I+ G +D N   +        G
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDIITGFVDPNAEEDLAPTATNVG 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESY 271
           ++ ++E+    +    +    + +      L   KFS +   ++K R A +  G +    
Sbjct: 183 SELSSEDLNDDDEEEDEDDDSEDDNSIDPELARQKFSELREQYEKTRVAIKTHGRSHAKA 242

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +   N+S      R   K  + L + +R  +++V   E+ I+++ V +  MP+ +FI +
Sbjct: 243 AEEILNLSEVFKQFRLVPKQFDYLVNNMRQMMDRVRTQERLIMKLCVEQSKMPKKNFITL 302

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE N  W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+M
Sbjct: 303 FTGNETNTTWFDAALAMAKPWGEKLKDVREDVERSLQKLHQIEEETGLTIEQVKDINRRM 362

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 363 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 422

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 423 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAE 482

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  +
Sbjct: 483 RMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATR 542

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 596


>gi|160867572|gb|ABX24195.1| hypothetical protein SARI_04418 [Salmonella enterica subsp. arizonae
            serovar 62:z4,z23:-]
          Length = 660

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 312/655 (47%), Positives = 431/655 (65%), Gaps = 18/655 (2%)

Query: 792  DKYDPDSYI--RKFGYKIFSKKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKER 843
            D+  PDS    ++  YK     N  S+ + +N   +       +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVGSYIVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 244

Query: 1022 STEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
              +  +    +        +  KF+ +   +   R   + +G +  +  +    +S    
Sbjct: 245  EEDGDDDAADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSHAAAQEEILKLSEVFK 304

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +
Sbjct: 305  QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+
Sbjct: 365  AAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 424

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 425  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 484

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK+
Sbjct: 485  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 544

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+K
Sbjct: 545  LKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAK 604

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 605  VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 659



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/637 (47%), Positives = 421/637 (66%), Gaps = 16/637 (2%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVGSYIVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588
           EP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L  LT RE+KVLRMR
Sbjct: 550 EPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMR 609

Query: 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           FGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>gi|219681993|ref|YP_002468377.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Tuc7
            (Acyrthosiphon pisum)]
 gi|219621726|gb|ACL29882.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
            (Acyrthosiphon pisum)]
          Length = 612

 Score =  591 bits (1523), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 318/630 (50%), Positives = 427/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPN---------- 171

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 1049
                  E+I +  ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 172  -----AEEIFL-PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 1050 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226  QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 1158
            I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286  IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFVSVK 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462  LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  577 bits (1487), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/617 (50%), Positives = 418/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPN---------- 171

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 259
                 E+I +  ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 172 -----AEEIFL-PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 260 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226 QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 368
           I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286 IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFVSVK 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462 LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|414562416|ref|YP_005617607.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
            (Acyrthosiphon pisum)]
 gi|311086952|gb|ADP67032.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
            (Acyrthosiphon pisum)]
          Length = 612

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 316/630 (50%), Positives = 424/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPNAEQ------- 174

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 1049
                     +   ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 175  ---------IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 1050 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226  QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 1158
            I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286  IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462  LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/617 (50%), Positives = 415/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPNAEQ------- 174

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 259
                    +   ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 175 ---------IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 260 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226 QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 368
           I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286 IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462 LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|90580773|ref|ZP_01236576.1| RNA polymerase sigma factor [Photobacterium angustum S14]
 gi|90438041|gb|EAS63229.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 616

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 312/617 (50%), Positives = 416/617 (67%), Gaps = 19/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N  +       +  
Sbjct: 123  IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---------------KFSNISFHFDKMRKAF 1051
            +     L ES   D   +  +    E                  KF  +   +DKM  A 
Sbjct: 183  SE----LSESDLEDEDKDLEDDEDAEDSDEEEDDGSIDPELAREKFLELRQAYDKMALAI 238

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            E  G  + +   A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+  
Sbjct: 239  ETNGRQNATTEVAVEELSEVFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 298

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  F+ +F  NE + +W+D        Y   L      ++    KL  L+ +  L +
Sbjct: 299  KMPKKTFVSLFAGNESSQDWIDEALNSGKPYAERLKAYEEDLRRSSLKLRMLEEETGLSI 358

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359  ERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA
Sbjct: 479  REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAA 538

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               ++R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539  TATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 599  RKLRHPSRSDVLRSFLD 615



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 407/604 (67%), Gaps = 19/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N  +       +  
Sbjct: 123 IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---------------KFSNISFHFDKMRKAF 261
           +     L ES   D   +  +    E                  KF  +   +DKM  A 
Sbjct: 183 SE----LSESDLEDEDKDLEDDEDAEDSDEEEDDGSIDPELAREKFLELRQAYDKMALAI 238

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           E  G  + +   A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+  
Sbjct: 239 ETNGRQNATTEVAVEELSEVFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 298

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  F+ +F  NE + +W+D        Y   L      ++    KL  L+ +  L +
Sbjct: 299 KMPKKTFVSLFAGNESSQDWIDEALNSGKPYAERLKAYEEDLRRSSLKLRMLEEETGLSI 358

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359 ERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA
Sbjct: 479 REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAA 538

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              ++R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539 TATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 622 RKLR 625
           RKLR
Sbjct: 599 RKLR 602


>gi|421729243|ref|ZP_16168388.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca M5al]
 gi|423125842|ref|ZP_17113521.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5250]
 gi|376398417|gb|EHT11043.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5250]
 gi|410369970|gb|EKP24706.1| RNA polymerase sigma factor RpoD [Klebsiella oxytoca M5al]
          Length = 614

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 417/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 408/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|440286101|ref|YP_007338866.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacteriaceae bacterium
            strain FGI 57]
 gi|440045623|gb|AGB76681.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacteriaceae bacterium
            strain FGI 57]
          Length = 613

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 415/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +   +  ++    D   +        S+       KF+ +   ++  R   + +G + 
Sbjct: 183  VGSELSQEEMDDDDEDEEDDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSETWFNAAVAMNKPWSEKLLDIKEDVQRSLMKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 406/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +   +  ++    D   +        S+       KF+ +   ++  R   + +G + 
Sbjct: 183 VGSELSQEEMDDDDEDEEDDDDSSDDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSETWFNAAVAMNKPWSEKLLDIKEDVQRSLMKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|21672345|ref|NP_660412.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
            (Schizaphis graminum)]
 gi|401010|sp|P32001.1|RPOD_BUCAP RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|144139|gb|AAA73234.1| sigma factor [Buchnera aphidicola]
 gi|21622948|gb|AAM67623.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
            (Schizaphis graminum)]
          Length = 617

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 315/633 (49%), Positives = 423/633 (66%), Gaps = 52/633 (8%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT++E+ND LPE+IID E I+ II+    M I V E   D +
Sbjct: 4    NPKSQLKLLVTHGKEQGYLTYAEVNDHLPEEIIDSEQIDDIIQMINDMGIQVVEEAPDAD 63

Query: 888  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
             L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64   DLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  ++S  P  I  +L   D+I   +I++ +I+ G +D N           
Sbjct: 123  KRIEEGINQVQSSVSEYPEAITYLLEQYDRIKTGQIRLSDIITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESSSA-DLSTEQLEKLKYESLI------------------------KFSN 1039
                 E+I   S+SA  + +E L+ +  +S                          KF  
Sbjct: 172  ----AEEIFSHSTSAIHIGSEILDNITNDSNENEDENEDENEDEDENSIDPELANEKFRE 227

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   +       + +  N +  +    N+S      R   K  + L + +RN +N+V + 
Sbjct: 228  LRKQYTNTSNTIKNKNRNHQDSLLEIYNLSEIFKQFRLVPKQFDHLVNNMRNMMNRVRKQ 287

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE---- 1155
            E++I+++ + +C +P+  F+K+F   E + NW   E       N    + +  IKE    
Sbjct: 288  ERKIMKLCIEECKIPKKIFLKIFSGKETDQNWFKKE----QSSNQSWSKKLEEIKEKVFS 343

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
              +KL  ++ +  L +  ++DIN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 344  SMKKLKQIEKETGLTIEQVKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGL 403

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 404  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 463

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 464  INKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHL 523

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 524  GDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQ 583

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            FDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 584  FDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 616



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 308/620 (49%), Positives = 414/620 (66%), Gaps = 52/620 (8%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT++E+ND LPE+IID E I+ II+    M I V E   D +
Sbjct: 4   NPKSQLKLLVTHGKEQGYLTYAEVNDHLPEEIIDSEQIDDIIQMINDMGIQVVEEAPDAD 63

Query: 98  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
            L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64  DLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  ++S  P  I  +L   D+I   +I++ +I+ G +D N           
Sbjct: 123 KRIEEGINQVQSSVSEYPEAITYLLEQYDRIKTGQIRLSDIITGFVDPN----------- 171

Query: 215 KNNNEEKILIESSSA-DLSTEQLEKLKYESLI------------------------KFSN 249
                E+I   S+SA  + +E L+ +  +S                          KF  
Sbjct: 172 ----AEEIFSHSTSAIHIGSEILDNITNDSNENEDENEDENEDEDENSIDPELANEKFRE 227

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   +       + +  N +  +    N+S      R   K  + L + +RN +N+V + 
Sbjct: 228 LRKQYTNTSNTIKNKNRNHQDSLLEIYNLSEIFKQFRLVPKQFDHLVNNMRNMMNRVRKQ 287

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE---- 365
           E++I+++ + +C +P+  F+K+F   E + NW   E       N    + +  IKE    
Sbjct: 288 ERKIMKLCIEECKIPKKIFLKIFSGKETDQNWFKKE----QSSNQSWSKKLEEIKEKVFS 343

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
             +KL  ++ +  L +  ++DIN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 344 SMKKLKQIEKETGLTIEQVKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGL 403

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 404 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 463

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 464 INKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHL 523

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDFIED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 524 GDFIEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQ 583

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 584 FDVTRERIRQIEAKALRKLR 603


>gi|237729995|ref|ZP_04560476.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
 gi|226908601|gb|EEH94519.1| RNA polymerase sigma-70 factor [Citrobacter sp. 30_2]
          Length = 660

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/621 (48%), Positives = 418/621 (67%), Gaps = 10/621 (1%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 39   IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 98

Query: 878  SVSEHVLDTETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
             V E   D + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELL
Sbjct: 99   QVMEEAPDADDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELL 158

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N  
Sbjct: 159  TREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAE 218

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKM 1047
             +      +  +   +  ++    +   +  +    +        +  KF  +   ++  
Sbjct: 219  EDMAPTATHVGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFGELRTQYEIT 278

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ 
Sbjct: 279  RDTIKAKGRSHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLC 338

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V +C MP+ +FI +F  NE +  W +    +   ++  L      +    QKL  ++ + 
Sbjct: 339  VEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEET 398

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 399  GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 458

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 459  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 518

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 519  QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 578

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 579  LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 638

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 639  AKALRKLRHPSRSEVLRSFLD 659



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/608 (48%), Positives = 409/608 (67%), Gaps = 10/608 (1%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 39  IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 98

Query: 88  SVSEHVLDTETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
            V E   D + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELL
Sbjct: 99  QVMEEAPDADDLLLAETSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELL 158

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N  
Sbjct: 159 TREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAE 218

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKM 257
            +      +  +   +  ++    +   +  +    +        +  KF  +   ++  
Sbjct: 219 EDMAPTATHVGSELSQEEMDDDEDEDEEDGDDDSSDDDNSIDPELAREKFGELRTQYEIT 278

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ 
Sbjct: 279 RDTIKAKGRSHAAAQEEIQKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLC 338

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V +C MP+ +FI +F  NE +  W +    +   ++  L      +    QKL  ++ + 
Sbjct: 339 VEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRGLQKLQQIEEET 398

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 399 GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 458

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 459 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 518

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 519 QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 578

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 579 LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 638

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 639 AKALRKLR 646


>gi|384225867|ref|YP_005617030.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. TLW03
            (Acyrthosiphon pisum)]
 gi|384226923|ref|YP_005618673.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LL01
            (Acyrthosiphon pisum)]
 gi|311085799|gb|ADP65881.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LL01
            (Acyrthosiphon pisum)]
 gi|311086374|gb|ADP66455.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. TLW03
            (Acyrthosiphon pisum)]
          Length = 612

 Score =  590 bits (1522), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 318/630 (50%), Positives = 427/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPN---------- 171

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 1049
                  E+I +  ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 172  -----AEEIFL-PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 1050 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226  QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 1158
            I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286  IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462  LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/617 (50%), Positives = 418/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPN---------- 171

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 259
                 E+I +  ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 172 -----AEEIFL-PTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 260 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226 QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 368
           I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286 IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462 LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|401765267|ref|YP_006580274.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp. cloacae
            ENHKU01]
 gi|400176801|gb|AFP71650.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp. cloacae
            ENHKU01]
          Length = 614

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 305/621 (49%), Positives = 419/621 (67%), Gaps = 29/621 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ + 
Sbjct: 303  FITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKDDVYRGLQKLHQIEEET 352

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353  GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473  QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533  LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 593  AKALRKLRHPSRSEVLRSFLD 613



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 298/608 (49%), Positives = 410/608 (67%), Gaps = 29/608 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ + 
Sbjct: 303 FITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKDDVYRGLQKLHQIEEET 352

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 353 GLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 412

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 413 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 472

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 473 QEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 532

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 533 LDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 593 AKALRKLR 600


>gi|431929985|ref|YP_007243031.1| sigma-70 family RNA polymerase sigma factor [Thioflavicoccus mobilis
            8321]
 gi|431828288|gb|AGA89401.1| RNA polymerase sigma factor, sigma-70 family [Thioflavicoccus mobilis
            8321]
          Length = 612

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 306/598 (51%), Positives = 414/598 (69%), Gaps = 5/598 (0%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 894
            LI  GKE+G+LT++E+ND LP  I++ E IE I++    M I V E   D+    LS+  
Sbjct: 13   LIAKGKEQGFLTYTEVNDHLPPGIVEPEQIEDIVRMINDMGIMVHETAPDSIDQTLSDSA 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             SDD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE++IAKRIE+GL  +
Sbjct: 73   VSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRIEDGLNQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            + A+S  P  I ++L   D++ + E+++ +++ G  D + ++        +         
Sbjct: 133  LTALSIYPRAIEKLLEIFDRVEREEVRLADVISGFNDGDETAEATTPSPAEAPQAADNSA 192

Query: 1015 ESSSADLSTEQLEKL----KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 1070
              S  D   +           E   +   +  H+  +++  E+ G + +   +A   +S 
Sbjct: 193  ADSDDDEDDDTTVADTGPDPEEVARRVQLLREHYAVLKQHLEQHGRDDQRSREAMQEVSE 252

Query: 1071 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 1130
              L  +  A    +L D LR+ I ++   EK ++   ++  GMPR  FI+ FP NE N  
Sbjct: 253  VFLQFKLVASIFHELTDLLRDTIERIRHQEKIVMTACIDTAGMPRKAFIESFPANETNPA 312

Query: 1131 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 1190
            W+D+       +   L  +   I+  Q+KL  L+ + VL +++++++NRKM  GE KAR+
Sbjct: 313  WLDDLLASGKPWAARLTESAADIRRAQRKLQELERENVLTISEIKEVNRKMSIGEAKARR 372

Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
            AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 373  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
            IRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +MEMPEEK+
Sbjct: 433  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELATRMEMPEEKV 492

Query: 1311 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 1370
            RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT R
Sbjct: 493  RKVLKIAKEPISMETPIGDDEDSHLGDFIEDAGVVSPIDSATMEGLREATQNMLASLTSR 552

Query: 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            E+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  +L+ FL+
Sbjct: 553  EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRLRSFLD 610



 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 303/593 (51%), Positives = 407/593 (68%), Gaps = 6/593 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-I 104
           LI  GKE+G+LT++E+ND LP  I++ E IE I++    M I V E   D+    LS+  
Sbjct: 13  LIAKGKEQGFLTYTEVNDHLPPGIVEPEQIEDIVRMINDMGIMVHETAPDSIDQTLSDSA 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            SDD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE++IAKRIE+GL  +
Sbjct: 73  VSDDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELQIAKRIEDGLNQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           + A+S  P  I ++L   D++ + E+++ +++ G  D + ++        +         
Sbjct: 133 LTALSIYPRAIEKLLEIFDRVEREEVRLADVISGFNDGDETAEATTPSPAEAPQAADNSA 192

Query: 225 ESSSADLSTEQLEKL----KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 280
             S  D   +           E   +   +  H+  +++  E+ G + +   +A   +S 
Sbjct: 193 ADSDDDEDDDTTVADTGPDPEEVARRVQLLREHYAVLKQHLEQHGRDDQRSREAMQEVSE 252

Query: 281 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 340
             L  +  A    +L D LR+ I ++   EK ++   ++  GMPR  FI+ FP NE N  
Sbjct: 253 VFLQFKLVASIFHELTDLLRDTIERIRHQEKIVMTACIDTAGMPRKAFIESFPANETNPA 312

Query: 341 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 400
           W+D+       +   L  +   I+  Q+KL  L+ + VL +++++++NRKM  GE KAR+
Sbjct: 313 WLDDLLASGKPWAARLTESAADIRRAQRKLQELERENVLTISEIKEVNRKMSIGEAKARR 372

Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
           AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
           IRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +MEMPEEK+
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMIQEMGREATPEELATRMEMPEEKV 492

Query: 521 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 580
           RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT R
Sbjct: 493 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDAGVVSPIDSATMEGLREATQNMLASLTSR 552

Query: 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           E+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 553 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDRL 605


>gi|260599325|ref|YP_003211896.1| RNA polymerase sigma factor RpoD [Cronobacter turicensis z3032]
 gi|260218502|emb|CBA33681.1| RNA polymerase sigma factor rpoD [Cronobacter turicensis z3032]
          Length = 614

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVADDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|15616680|ref|NP_239892.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. APS
            (Acyrthosiphon pisum)]
 gi|219681437|ref|YP_002467822.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. 5A
            (Acyrthosiphon pisum)]
 gi|257471112|ref|ZP_05635111.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. LSR1
            (Acyrthosiphon pisum)]
 gi|11134512|sp|P57163.1|RPOD_BUCAI RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|25288437|pir||B84936 RNA polymerase sigma factor rpoD [imported] - Buchnera sp.  (strain
            APS)
 gi|10038743|dbj|BAB12778.1| RNA polymerase sigma factor rpoD [Buchnera aphidicola str. APS
            (Acyrthosiphon pisum)]
 gi|219624280|gb|ACL30435.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
            (Acyrthosiphon pisum)]
          Length = 612

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 316/630 (50%), Positives = 424/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122  AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPNAEE------- 174

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 1049
                     +   ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 175  ---------IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 1050 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226  QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 1158
            I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286  IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462  LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/617 (50%), Positives = 415/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDIID E I+ II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTHGKEQGYLTYSEVNDHLPEDIIDSEQIDDIIQMINDMGIPVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+ I +D D E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLILNEINTDTD-EDAVEAATQVLSSVESELGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  ++S  P  I  +L   D++   +I++ +I+ G +D N          
Sbjct: 122 AKRIEEGINQVQCSVSEYPEAITYLLEQYDRVKTGQIRLSDIITGFVDPNAEE------- 174

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH--------------FDKMRK 259
                    +   ++  + +E L++ +     + +N   H              F ++R 
Sbjct: 175 ---------IFPPTAIHIGSELLDEQQNNEEDEENNQEDHEDDHSIDPELANEKFSELRI 225

Query: 260 AFEKEGYNSESYIKAHN-------NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            +       ++  + H        N+S      R   K  + L + +R+ + +V + E+ 
Sbjct: 226 QYNNTNNTIKNKNRTHKDSLLEIYNLSEVFKQFRLVPKQFDHLVNNMRHMMERVRKQERI 285

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQ 368
           I+++ V  C MP+ +FIK+FP  +IN  W   E     + N     N+  +KE      +
Sbjct: 286 IIKLCVEICKMPKKNFIKIFPIKKINYLWFIRE----QNTNQPWSENLKKVKEDVFISVK 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KLI ++ +  L +  ++DIN++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLIKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 462 LNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|242240773|ref|YP_002988954.1| RNA polymerase sigma factor RpoD [Dickeya dadantii Ech703]
 gi|242132830|gb|ACS87132.1| RNA polymerase, sigma 70 subunit, RpoD [Dickeya dadantii Ech703]
          Length = 612

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 417/609 (68%), Gaps = 7/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +         
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAAAAPEST 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 1059
              E + + +    +           ++ I       KF+ +   ++  R + +  G + +
Sbjct: 183  ELEGEEIEDEEEDEEEDGDNSDSDDDNSIDPELARQKFTELREQYEATRLSIKAHGRSHQ 242

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            S I   N +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+
Sbjct: 243  SAIDEINKLSEVFKQFRLVPKQFDLLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFM 302

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
             +F  NE ++ W +    +   ++  L      ++    KL  ++ +  L +  ++DINR
Sbjct: 303  TMFTGNETSIKWFEAALAMGKPWSEKLREVTDDVERSLLKLQQIEEETGLTIEQVKDINR 362

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483  AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 543  THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 602

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 603  SEVLRSFLD 611



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 299/596 (50%), Positives = 408/596 (68%), Gaps = 7/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +         
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAAAAPEST 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 269
             E + + +    +           ++ I       KF+ +   ++  R + +  G + +
Sbjct: 183 ELEGEEIEDEEEDEEEDGDNSDSDDDNSIDPELARQKFTELREQYEATRLSIKAHGRSHQ 242

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           S I   N +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+
Sbjct: 243 SAIDEINKLSEVFKQFRLVPKQFDLLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFM 302

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
            +F  NE ++ W +    +   ++  L      ++    KL  ++ +  L +  ++DINR
Sbjct: 303 TMFTGNETSIKWFEAALAMGKPWSEKLREVTDDVERSLLKLQQIEEETGLTIEQVKDINR 362

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483 AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|333982488|ref|YP_004511698.1| RNA polymerase sigma-70 subunit RpoD [Methylomonas methanica MC09]
 gi|333806529|gb|AEF99198.1| RNA polymerase, sigma 70 subunit, RpoD [Methylomonas methanica MC09]
          Length = 604

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/607 (50%), Positives = 414/607 (68%), Gaps = 27/607 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 893
            LI  GK +GYLT++E+ND LP DIID E I+ II     M I V E   D +  +++   
Sbjct: 13   LIAKGKAQGYLTYAEVNDHLPSDIIDPEQIDDIIGMINDMGIQVYEVAPDDDDSLITADT 72

Query: 894  -ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
             +++DDD E A  AAL++VDS+FGRT DP+++YMREMGSVELLTR+ E++IAKRIEEG +
Sbjct: 73   VVSADDDEEVAEVAALASVDSEFGRTTDPVRLYMREMGSVELLTREQELKIAKRIEEGQR 132

Query: 953  DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++ A++     +   +     ++  E   ++ ++V G +D +                +
Sbjct: 133  QVVAAVARSGFIVDSFIETFSGVADEESSTRLGDLVQGFVDYSDVDEV---------EVD 183

Query: 1011 KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYIK 1063
            ++ IE+ + D   E+++      +I +S +    D ++K       A +K GY  +   K
Sbjct: 184  EVEIEAPADDADDEEVK------VIDYSEVKEKVDLLKKSLKTAMAAVKKHGYGHDKSEK 237

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A + +S      ++T + ++++       I  + + E+Q+++  V +  MPR  FI  F 
Sbjct: 238  AFDALSEIFSQFKWTPQYLKRMTSVADELIAAIREQERQVMDACVKRTKMPRRDFINAFT 297

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
            ENE  LNW+D   +    Y   L  N   I+  QQKL +++    L + +L+ I R +  
Sbjct: 298  ENEAQLNWLDQFIQDNPKYADALNSNREKIQSAQQKLADIEAQHGLSIANLKQICRNISL 357

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 358  GEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 417

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQILQE G E  P  +A +M
Sbjct: 418  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQILQEMGREATPEELAERM 477

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ML+P ++A  A +R   +++
Sbjct: 478  EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSKMLSPVESATIAGLRESTQNV 537

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L
Sbjct: 538  LAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQL 597

Query: 1424 KIFLEGK 1430
            + FL+G+
Sbjct: 598  RCFLDGE 604



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/592 (50%), Positives = 402/592 (67%), Gaps = 27/592 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 103
           LI  GK +GYLT++E+ND LP DIID E I+ II     M I V E   D +  +++   
Sbjct: 13  LIAKGKAQGYLTYAEVNDHLPSDIIDPEQIDDIIGMINDMGIQVYEVAPDDDDSLITADT 72

Query: 104 -ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
            +++DDD E A  AAL++VDS+FGRT DP+++YMREMGSVELLTR+ E++IAKRIEEG +
Sbjct: 73  VVSADDDEEVAEVAALASVDSEFGRTTDPVRLYMREMGSVELLTREQELKIAKRIEEGQR 132

Query: 163 DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++ A++     +   +     ++  E   ++ ++V G +D +                +
Sbjct: 133 QVVAAVARSGFIVDSFIETFSGVADEESSTRLGDLVQGFVDYSDVDEV---------EVD 183

Query: 221 KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYIK 273
           ++ IE+ + D   E+++      +I +S +    D ++K       A +K GY  +   K
Sbjct: 184 EVEIEAPADDADDEEVK------VIDYSEVKEKVDLLKKSLKTAMAAVKKHGYGHDKSEK 237

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A + +S      ++T + ++++       I  + + E+Q+++  V +  MPR  FI  F 
Sbjct: 238 AFDALSEIFSQFKWTPQYLKRMTSVADELIAAIREQERQVMDACVKRTKMPRRDFINAFT 297

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
           ENE  LNW+D   +    Y   L  N   I+  QQKL +++    L + +L+ I R +  
Sbjct: 298 ENEAQLNWLDQFIQDNPKYADALNSNREKIQSAQQKLADIEAQHGLSIANLKQICRNISL 357

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 358 GEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 417

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQILQE G E  P  +A +M
Sbjct: 418 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQILQEMGREATPEELAERM 477

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ML+P ++A  A +R   +++
Sbjct: 478 EMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSKMLSPVESATIAGLRESTQNV 537

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 538 LAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 589


>gi|402840242|ref|ZP_10888711.1| RNA polymerase sigma factor RpoD [Klebsiella sp. OBRC7]
 gi|423104915|ref|ZP_17092617.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5242]
 gi|376381681|gb|EHS94417.1| RNA polymerase sigma factor rpoD [Klebsiella oxytoca 10-5242]
 gi|402287192|gb|EJU35652.1| RNA polymerase sigma factor RpoD [Klebsiella sp. OBRC7]
          Length = 614

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 417/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 408/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  N  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETNNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +   E  +    ++ I       KF+ +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEEEDDDSSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLLDVKEDVQRGLMKLQQIEQETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|429090134|ref|ZP_19152866.1| RNA polymerase sigma factor RpoD [Cronobacter universalis NCTC 9529]
 gi|426509937|emb|CCK17978.1| RNA polymerase sigma factor RpoD [Cronobacter universalis NCTC 9529]
          Length = 614

 Score =  590 bits (1521), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 416/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 407/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           + +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 NAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|170719016|ref|YP_001784175.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 2336]
 gi|168827145|gb|ACA32516.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 2336]
          Length = 621

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/628 (49%), Positives = 435/628 (69%), Gaps = 36/628 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPED++D + IE +I+    M I V E V D 
Sbjct: 3    QNKQSQLKLLIARGKEQGYLTYAEVNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN- 1004
            RIEEG+ ++  A+++ P  +  +L     + +  +++ +++ G +D N      +I+ + 
Sbjct: 122  RIEEGINEVQSAVAAYPKALNYLLEQYTLVEEGGMRLADLITGFVDPNAVVEEEIIEADD 181

Query: 1005 --KNNNEEKI-------------------LIESSSADLSTEQLEKLKYESLIKFSNISFH 1043
                ++EE +                    ++S S +    ++ + K+E+L         
Sbjct: 182  ILTEDDEEHVESNVDVNDEEEEEDSEDNSNVDSDSDNTIAPEVAREKFEAL------RIQ 235

Query: 1044 FDKMRKAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
              K   A EK G +   ++ +I+A  +I  +    R   K  + L + +R+ +  V Q E
Sbjct: 236  HQKTLAAIEKYGRSRKQAKDHIQALADIFTQ---FRLVPKQFDALVNYMRDMMKSVRQHE 292

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            +QI ++VV+   MP+ +F K+F  NE +  W+D     +  ++  L ++  ++++   +L
Sbjct: 293  RQIQKLVVDLAKMPKENFQKLFIGNESSEGWLDKLLLARKPWSERLIQHESAVRQSINQL 352

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
            + ++ +  L ++ +R+I  K+  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 353  LKIEQETNLTISQIREICDKVAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 412

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 413  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 472

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQ+LQ+ G E     +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 473  RISRQMLQKMGREATSEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 532

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D  +  P D+A   S+R+   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 533  DNTLELPLDSATAQSLRAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 592

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 593  ERIRQIEAKALRKLRHPSRSETLRSFLD 620



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 303/615 (49%), Positives = 426/615 (69%), Gaps = 36/615 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPED++D + IE +I+    M I V E V D 
Sbjct: 3   QNKQSQLKLLIARGKEQGYLTYAEVNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN- 214
           RIEEG+ ++  A+++ P  +  +L     + +  +++ +++ G +D N      +I+ + 
Sbjct: 122 RIEEGINEVQSAVAAYPKALNYLLEQYTLVEEGGMRLADLITGFVDPNAVVEEEIIEADD 181

Query: 215 --KNNNEEKI-------------------LIESSSADLSTEQLEKLKYESLIKFSNISFH 253
               ++EE +                    ++S S +    ++ + K+E+L         
Sbjct: 182 ILTEDDEEHVESNVDVNDEEEEEDSEDNSNVDSDSDNTIAPEVAREKFEAL------RIQ 235

Query: 254 FDKMRKAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
             K   A EK G +   ++ +I+A  +I  +    R   K  + L + +R+ +  V Q E
Sbjct: 236 HQKTLAAIEKYGRSRKQAKDHIQALADIFTQ---FRLVPKQFDALVNYMRDMMKSVRQHE 292

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           +QI ++VV+   MP+ +F K+F  NE +  W+D     +  ++  L ++  ++++   +L
Sbjct: 293 RQIQKLVVDLAKMPKENFQKLFIGNESSEGWLDKLLLARKPWSERLIQHESAVRQSINQL 352

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
           + ++ +  L ++ +R+I  K+  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 353 LKIEQETNLTISQIREICDKVAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 412

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 413 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 472

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQ+LQ+ G E     +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 473 RISRQMLQKMGREATSEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 532

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D  +  P D+A   S+R+   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 533 DNTLELPLDSATAQSLRAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 592

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 593 ERIRQIEAKALRKLR 607


>gi|104779687|ref|YP_606185.1| RNA polymerase sigma factor RpoD [Pseudomonas entomophila L48]
 gi|95108674|emb|CAK13368.1| sigma D (sigma 70) factor of RNA polymerase [Pseudomonas entomophila
            L48]
          Length = 616

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 311/606 (51%), Positives = 421/606 (69%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  I+   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130  REVMGAIAHFPGTVDYIISEYDRVTAEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              ++   E      S++  E+ +       +  +F  ++       K  +K G      I
Sbjct: 190  AAKEEEDEDDENAESSDDEEEAESGPDPVVAAQRFGAVNDQLVITLKVLKKHGRTHAESI 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   +++  + I+   K  + L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250  GAMQALADLFMPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310  PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 550  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSEH 609

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 610  LRSFLD 615



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/593 (51%), Positives = 412/593 (69%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  I+   D+++    ++ +++ G ID +      +    I G K  
Sbjct: 130 REVMGAIAHFPGTVDYIISEYDRVTAEGGRLSDVLSGYIDPDDNIAAPTEEVPIPGAKAA 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             ++   E      S++  E+ +       +  +F  ++       K  +K G      I
Sbjct: 190 AAKEEEDEDDENAESSDDEEEAESGPDPVVAAQRFGAVNDQLVITLKVLKKHGRTHAESI 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   +++  + I+   K  + L + +R+ ++++ Q E+ I+++ V    MPR  F+++F
Sbjct: 250 GAMQALADLFMPIKLVPKQFDALVERVRSALDRLRQQERAIMQLCVRDARMPRADFLRLF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M 
Sbjct: 310 PSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +D
Sbjct: 490 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRD 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|330448778|ref|ZP_08312425.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
            [Photobacterium leiognathi subsp. mandapamensis
            svers.1.1.]
 gi|328492969|dbj|GAA06922.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor
            [Photobacterium leiognathi subsp. mandapamensis
            svers.1.1.]
          Length = 616

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 313/613 (51%), Positives = 416/613 (67%), Gaps = 11/613 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E++I +I+ G +D N  +       +  
Sbjct: 123  IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRITDIISGFVDPNEEATAAPTATHIG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEG 1055
            +   +  +E    DL  +  E    E              KF  +   +DKM  A +  G
Sbjct: 183  SELSETDLEDEDKDLEDDDDEDADSEDEDDGSIDPELAREKFLELRNAYDKMALAIDTNG 242

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               +    A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+   MP+
Sbjct: 243  RQDKQTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDAMDKVRTNERLIMRMCVDNSKMPK 302

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              F+ +F  NE N +W+D        Y   L      ++    KL  L+ +  L +  ++
Sbjct: 303  KTFVTLFAGNEANQDWIDEALNSGKPYAERLKTYEEDLRRSAIKLRMLEEETGLSIERIK 362

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363  DISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPL 482

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   +
Sbjct: 483  PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATATN 542

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543  LRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 603  HPSRSDVLRSFLD 615



 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 306/600 (51%), Positives = 407/600 (67%), Gaps = 11/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E++I +I+ G +D N  +       +  
Sbjct: 123 IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRITDIISGFVDPNEEATAAPTATHIG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEG 265
           +   +  +E    DL  +  E    E              KF  +   +DKM  A +  G
Sbjct: 183 SELSETDLEDEDKDLEDDDDEDADSEDEDDGSIDPELAREKFLELRNAYDKMALAIDTNG 242

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              +    A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+   MP+
Sbjct: 243 RQDKQTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDAMDKVRTNERLIMRMCVDNSKMPK 302

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             F+ +F  NE N +W+D        Y   L      ++    KL  L+ +  L +  ++
Sbjct: 303 KTFVTLFAGNEANQDWIDEALNSGKPYAERLKTYEEDLRRSAIKLRMLEEETGLSIERIK 362

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363 DISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPL 482

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   +
Sbjct: 483 PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATATN 542

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 LRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|445135611|ref|ZP_21383363.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Gallinarum str. 9184]
 gi|444845812|gb|ELX71000.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Gallinarum str. 9184]
          Length = 615

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|378578674|ref|ZP_09827349.1| RNA polymerase, sigma 70 (sigma D) factor [Pantoea stewartii subsp.
            stewartii DC283]
 gi|377818954|gb|EHU02035.1| RNA polymerase, sigma 70 (sigma D) factor [Pantoea stewartii subsp.
            stewartii DC283]
          Length = 609

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 307/607 (50%), Positives = 414/607 (68%), Gaps = 6/607 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPN-AEEDLAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESY 1061
               +E      +   D   E  +    +  +   KFS++   ++  R   + +G +  + 
Sbjct: 182  HVGSELSEEDRNDDDDDDEESDDDCSIDPELAREKFSDLRTQYETTRDVIKSKGRSHAAS 241

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +    N+S+     R   K  + L + +R  + +V   E+ I+++ +  C MP+ +FI +
Sbjct: 242  VAEIQNLSDVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMPKKNFITL 301

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+M
Sbjct: 302  FTGNETNESWFKAALAMNKPWSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQVKDINRRM 361

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 362  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 421

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 422  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAE 481

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS   
Sbjct: 482  RMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATH 541

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 542  DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 601

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 602  VLRSFLD 608



 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/594 (50%), Positives = 405/594 (68%), Gaps = 6/594 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPN-AEEDLAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESY 271
              +E      +   D   E  +    +  +   KFS++   ++  R   + +G +  + 
Sbjct: 182 HVGSELSEEDRNDDDDDDEESDDDCSIDPELAREKFSDLRTQYETTRDVIKSKGRSHAAS 241

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +    N+S+     R   K  + L + +R  + +V   E+ I+++ +  C MP+ +FI +
Sbjct: 242 VAEIQNLSDVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIEVCKMPKKNFITL 301

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+M
Sbjct: 302 FTGNETNESWFKAALAMNKPWSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQVKDINRRM 361

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 362 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 421

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 422 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAE 481

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS   
Sbjct: 482 RMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSATH 541

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 595


>gi|354725249|ref|ZP_09039464.1| RNA polymerase sigma factor RpoD [Enterobacter mori LMG 25706]
          Length = 613

 Score =  590 bits (1520), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 416/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +   +  ++    +   E+ +     S+       KF  +   ++  R   + +G + 
Sbjct: 183  VGSELSQEEMDDDEDEDEEEEDDSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSETWFNAAIAMNKPWSEKLHDVKDDVQRGLMKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 407/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +   +  ++    +   E+ +     S+       KF  +   ++  R   + +G + 
Sbjct: 183 VGSELSQEEMDDDEDEDEEEEDDSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      ++    KL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSETWFNAAIAMNKPWSEKLHDVKDDVQRGLMKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|429093626|ref|ZP_19156207.1| RNA polymerase sigma factor RpoD [Cronobacter dublinensis 1210]
 gi|426741454|emb|CCJ82320.1| RNA polymerase sigma factor RpoD [Cronobacter dublinensis 1210]
          Length = 614

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 414/611 (67%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183  VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 405/598 (67%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++    +      +    ++ I       KF  +   ++  R   + +G +
Sbjct: 183 VGSELSQEEMDDDEDEDEESDDDSSDDDNSIDPELAREKFGELRTQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAASQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKMCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEDVHRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|39546362|ref|NP_462126.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. LT2]
 gi|161616204|ref|YP_001590169.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Paratyphi B str. SPB7]
 gi|167551873|ref|ZP_02345626.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Saintpaul str. SARA29]
 gi|167990234|ref|ZP_02571334.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar 4,[5],12:i:- str. CVM23701]
 gi|168237909|ref|ZP_02662967.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Schwarzengrund str. SL480]
 gi|168243042|ref|ZP_02667974.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. SL486]
 gi|168262827|ref|ZP_02684800.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Hadar str. RI_05P066]
 gi|168463576|ref|ZP_02697493.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. SL317]
 gi|194445988|ref|YP_002042478.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. SL254]
 gi|194451693|ref|YP_002047209.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. SL476]
 gi|194472915|ref|ZP_03078899.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Kentucky str. CVM29188]
 gi|194736124|ref|YP_002116168.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Schwarzengrund str. CVM19633]
 gi|197251872|ref|YP_002148141.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SL483]
 gi|197264102|ref|ZP_03164176.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Saintpaul str. SARA23]
 gi|198242489|ref|YP_002217192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. CT_02021853]
 gi|200389116|ref|ZP_03215728.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Virchow str. SL491]
 gi|204928094|ref|ZP_03219294.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Javiana str. GA_MM04042433]
 gi|207858469|ref|YP_002245120.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. P125109]
 gi|213425630|ref|ZP_03358380.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. E02-1180]
 gi|213586893|ref|ZP_03368719.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. E98-0664]
 gi|213646106|ref|ZP_03376159.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. J185]
 gi|213865054|ref|ZP_03387173.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. M223]
 gi|238910014|ref|ZP_04653851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Tennessee str. CDC07-0191]
 gi|374979234|ref|ZP_09720573.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. TN061786]
 gi|378701116|ref|YP_005183073.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. SL1344]
 gi|378956833|ref|YP_005214320.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Gallinarum/pullorum str. RKS5078]
 gi|378961310|ref|YP_005218796.1| RNA polymerase sigma factor rpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. P-stx-12]
 gi|378985810|ref|YP_005248966.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. T000240]
 gi|383497870|ref|YP_005398559.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. 798]
 gi|386592907|ref|YP_006089307.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. B182]
 gi|409994562|ref|NP_806814.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. Ty2]
 gi|416507097|ref|ZP_11735130.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. SARB31]
 gi|416515950|ref|ZP_11738900.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. ATCC BAA710]
 gi|416527058|ref|ZP_11742896.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. LQC 10]
 gi|416534010|ref|ZP_11746828.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. SARB30]
 gi|416549743|ref|ZP_11755586.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 29N]
 gi|416557454|ref|ZP_11759531.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 42N]
 gi|416568407|ref|ZP_11764759.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 4441 H]
 gi|418514564|ref|ZP_13080764.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Pomona str. ATCC 10729]
 gi|418760988|ref|ZP_13317140.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35185]
 gi|418766025|ref|ZP_13322104.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35199]
 gi|418771351|ref|ZP_13327358.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21539]
 gi|418773881|ref|ZP_13329854.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 33953]
 gi|418778313|ref|ZP_13334223.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35188]
 gi|418783509|ref|ZP_13339356.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21559]
 gi|418788635|ref|ZP_13344428.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19447]
 gi|418794325|ref|ZP_13350046.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19449]
 gi|418797525|ref|ZP_13353211.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19567]
 gi|418801894|ref|ZP_13357526.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35202]
 gi|418806427|ref|ZP_13361999.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21550]
 gi|418810587|ref|ZP_13366127.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22513]
 gi|418818203|ref|ZP_13373682.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21538]
 gi|418823271|ref|ZP_13378680.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22425]
 gi|418826732|ref|ZP_13381926.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22462]
 gi|418831165|ref|ZP_13386123.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM N18486]
 gi|418837102|ref|ZP_13391977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM N1543]
 gi|418842364|ref|ZP_13397174.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21554]
 gi|418846941|ref|ZP_13401706.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19443]
 gi|418847831|ref|ZP_13402571.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 37978]
 gi|418855995|ref|ZP_13410643.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19593]
 gi|418857758|ref|ZP_13412383.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19470]
 gi|418862767|ref|ZP_13417306.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19536]
 gi|418869570|ref|ZP_13424003.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 4176]
 gi|419731466|ref|ZP_14258379.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41579]
 gi|419735921|ref|ZP_14262794.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41563]
 gi|419739690|ref|ZP_14266435.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41573]
 gi|419742086|ref|ZP_14268764.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41566]
 gi|419748917|ref|ZP_14275407.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41565]
 gi|419786851|ref|ZP_14312566.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. Levine 1]
 gi|419793243|ref|ZP_14318866.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. Levine 15]
 gi|421360800|ref|ZP_15811076.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 622731-39]
 gi|421363574|ref|ZP_15813816.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639016-6]
 gi|421369897|ref|ZP_15820072.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 640631]
 gi|421374341|ref|ZP_15824472.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-0424]
 gi|421383609|ref|ZP_15833647.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 485549-17]
 gi|421384745|ref|ZP_15834768.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 596866-22]
 gi|421389613|ref|ZP_15839596.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 596866-70]
 gi|421396899|ref|ZP_15846824.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629164-26]
 gi|421399678|ref|ZP_15849573.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629164-37]
 gi|421405833|ref|ZP_15855658.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639672-46]
 gi|421408640|ref|ZP_15858439.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639672-50]
 gi|421414730|ref|ZP_15864466.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-1427]
 gi|421417668|ref|ZP_15867378.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-2659]
 gi|421421006|ref|ZP_15870682.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 78-1757]
 gi|421428652|ref|ZP_15878263.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22510-1]
 gi|421435476|ref|ZP_15885012.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648905 5-18]
 gi|421439899|ref|ZP_15889379.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 6-18]
 gi|421444043|ref|ZP_15893482.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 50-3079]
 gi|421449516|ref|ZP_15898900.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 58-6482]
 gi|421573093|ref|ZP_16018738.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00322]
 gi|421577073|ref|ZP_16022663.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00325]
 gi|421579571|ref|ZP_16025134.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00326]
 gi|421583423|ref|ZP_16028947.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00328]
 gi|422027434|ref|ZP_16373776.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm1]
 gi|422032472|ref|ZP_16378584.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm2]
 gi|423141745|ref|ZP_17129383.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. houtenae
            str. ATCC BAA-1581]
 gi|427554172|ref|ZP_18929074.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm8]
 gi|427571814|ref|ZP_18933789.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm9]
 gi|427592498|ref|ZP_18938588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm3]
 gi|427616324|ref|ZP_18943480.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm4]
 gi|427639980|ref|ZP_18948358.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm6]
 gi|427657451|ref|ZP_18953103.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm10]
 gi|427662767|ref|ZP_18958068.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm11]
 gi|427676650|ref|ZP_18962883.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm12]
 gi|427800480|ref|ZP_18968231.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm5]
 gi|436602306|ref|ZP_20513126.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22704]
 gi|436747625|ref|ZP_20520041.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE30663]
 gi|436799873|ref|ZP_20524159.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CHS44]
 gi|436807275|ref|ZP_20527318.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1882]
 gi|436818166|ref|ZP_20534799.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1884]
 gi|436832389|ref|ZP_20536679.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1594]
 gi|436853265|ref|ZP_20543290.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1566]
 gi|436860948|ref|ZP_20548132.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1580]
 gi|436867824|ref|ZP_20552978.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1543]
 gi|436873169|ref|ZP_20556051.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1441]
 gi|436880161|ref|ZP_20559920.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1810]
 gi|436891794|ref|ZP_20566494.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1558]
 gi|436899300|ref|ZP_20570711.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1018]
 gi|436902811|ref|ZP_20573275.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1010]
 gi|436915106|ref|ZP_20579953.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1729]
 gi|436919805|ref|ZP_20582586.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0895]
 gi|436929097|ref|ZP_20588303.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0899]
 gi|436938290|ref|ZP_20593077.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1457]
 gi|436946149|ref|ZP_20597977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1747]
 gi|436955612|ref|ZP_20602487.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0968]
 gi|436966344|ref|ZP_20607013.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1444]
 gi|436970435|ref|ZP_20608965.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1445]
 gi|436979907|ref|ZP_20613052.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1559]
 gi|436993685|ref|ZP_20618478.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1565]
 gi|437009448|ref|ZP_20623825.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1808]
 gi|437022589|ref|ZP_20628538.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1811]
 gi|437028542|ref|ZP_20630634.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0956]
 gi|437042811|ref|ZP_20636324.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1455]
 gi|437050486|ref|ZP_20640631.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1575]
 gi|437061718|ref|ZP_20647084.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1725]
 gi|437066634|ref|ZP_20649696.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1745]
 gi|437074141|ref|ZP_20653583.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1791]
 gi|437083225|ref|ZP_20658968.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1795]
 gi|437097967|ref|ZP_20665422.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 576709]
 gi|437110752|ref|ZP_20668098.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 635290-58]
 gi|437124989|ref|ZP_20673737.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-16]
 gi|437129710|ref|ZP_20676186.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-19]
 gi|437146339|ref|ZP_20686128.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-9]
 gi|437159671|ref|ZP_20694069.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE15-1]
 gi|437169134|ref|ZP_20699527.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_N202]
 gi|437173351|ref|ZP_20701677.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_56-3991]
 gi|437184671|ref|ZP_20708536.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_76-3618]
 gi|437201078|ref|ZP_20711779.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 13183-1]
 gi|437264915|ref|ZP_20720191.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_81-2490]
 gi|437269227|ref|ZP_20722470.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SL909]
 gi|437277439|ref|ZP_20726798.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SL913]
 gi|437296826|ref|ZP_20732627.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_69-4941]
 gi|437316046|ref|ZP_20737734.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 638970-15]
 gi|437327880|ref|ZP_20740822.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 17927]
 gi|437341947|ref|ZP_20745070.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CHS4]
 gi|437350372|ref|ZP_20747323.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22558]
 gi|437417704|ref|ZP_20754123.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 22-17]
 gi|437445947|ref|ZP_20758669.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 40-18]
 gi|437463551|ref|ZP_20763233.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 561362 1-1]
 gi|437480886|ref|ZP_20768591.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642044 4-1]
 gi|437492379|ref|ZP_20771610.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642046 4-7]
 gi|437504726|ref|ZP_20775208.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648898 4-5]
 gi|437538270|ref|ZP_20781969.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648899 3-17]
 gi|437567274|ref|ZP_20787545.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648900 1-16]
 gi|437580671|ref|ZP_20792074.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 1-17]
 gi|437588169|ref|ZP_20793809.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 39-2]
 gi|437604906|ref|ZP_20799085.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648902 6-8]
 gi|437619527|ref|ZP_20803679.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648903 1-6]
 gi|437646069|ref|ZP_20808964.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648904 3-6]
 gi|437665555|ref|ZP_20814706.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 653049 13-19]
 gi|437679849|ref|ZP_20818153.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642044 8-1]
 gi|437700110|ref|ZP_20823697.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 561362 9-7]
 gi|437702347|ref|ZP_20824129.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 42-20]
 gi|437729604|ref|ZP_20830736.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 16-16]
 gi|437761736|ref|ZP_20834740.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 76-2651]
 gi|437837915|ref|ZP_20845908.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SARB17]
 gi|437865341|ref|ZP_20848096.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 6.0562-1]
 gi|438057339|ref|ZP_20856523.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 50-5646]
 gi|438095444|ref|ZP_20862042.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 81-2625]
 gi|438101889|ref|ZP_20864716.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 62-1976]
 gi|438116459|ref|ZP_20870978.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 53-407]
 gi|438140993|ref|ZP_20874991.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Pullorum str. ATCC 9120]
 gi|440765148|ref|ZP_20944169.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH11G1113]
 gi|440770486|ref|ZP_20949435.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH08SF124]
 gi|440775172|ref|ZP_20954057.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH10GFN094]
 gi|445142847|ref|ZP_21386258.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. SL1438]
 gi|445151081|ref|ZP_21390031.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. HWS51]
 gi|445169473|ref|ZP_21395276.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE8a]
 gi|445180170|ref|ZP_21398117.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 20037]
 gi|445226451|ref|ZP_21403932.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE10]
 gi|445241208|ref|ZP_21407649.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 436]
 gi|445330756|ref|ZP_21413944.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 18569]
 gi|452122967|ref|YP_007473215.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Javiana str. CFSAN001992]
 gi|61234163|sp|P0A2E3.1|RPOD_SALTY RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|61234169|sp|P0A2E4.1|RPOD_SALTI RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|154406|gb|AAA27242.1| rpoD protein [Salmonella enterica subsp. enterica serovar
            Typhimurium]
 gi|161365568|gb|ABX69336.1| hypothetical protein SPAB_04007 [Salmonella enterica subsp. enterica
            serovar Paratyphi B str. SPB7]
 gi|194404651|gb|ACF64873.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. SL254]
 gi|194409997|gb|ACF70216.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. SL476]
 gi|194459279|gb|EDX48118.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Kentucky str. CVM29188]
 gi|194711626|gb|ACF90847.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Schwarzengrund str. CVM19633]
 gi|195633147|gb|EDX51561.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. SL317]
 gi|197215575|gb|ACH52972.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SL483]
 gi|197242357|gb|EDY24977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Saintpaul str. SARA23]
 gi|197289083|gb|EDY28452.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Schwarzengrund str. SL480]
 gi|197937005|gb|ACH74338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. CT_02021853]
 gi|199606214|gb|EDZ04759.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Virchow str. SL491]
 gi|204322416|gb|EDZ07613.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Javiana str. GA_MM04042433]
 gi|205323318|gb|EDZ11157.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Saintpaul str. SARA29]
 gi|205331247|gb|EDZ18011.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar 4,[5],12:i:- str. CVM23701]
 gi|205337819|gb|EDZ24583.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. SL486]
 gi|205348629|gb|EDZ35260.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Hadar str. RI_05P066]
 gi|206710272|emb|CAR34630.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Enteritidis str. P125109]
 gi|301159764|emb|CBW19283.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. SL1344]
 gi|312914239|dbj|BAJ38213.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. T000240]
 gi|321225894|gb|EFX50948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. TN061786]
 gi|357207444|gb|AET55490.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Gallinarum/pullorum str. RKS5078]
 gi|363553899|gb|EHL38144.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. SARB31]
 gi|363556713|gb|EHL40926.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. LQC 10]
 gi|363563041|gb|EHL47122.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. ATCC BAA710]
 gi|363567634|gb|EHL51632.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. SARB30]
 gi|363569692|gb|EHL53642.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 29N]
 gi|363577752|gb|EHL61571.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 4441 H]
 gi|363578554|gb|EHL62359.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 42N]
 gi|366078815|gb|EHN42813.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Pomona str. ATCC 10729]
 gi|374355182|gb|AEZ46943.1| RNA polymerase sigma factor rpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. P-stx-12]
 gi|379050917|gb|EHY68809.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. houtenae
            str. ATCC BAA-1581]
 gi|380464691|gb|AFD60094.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Typhimurium str. 798]
 gi|381291647|gb|EIC32884.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41579]
 gi|381294245|gb|EIC35385.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41563]
 gi|381298269|gb|EIC39350.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41573]
 gi|381312913|gb|EIC53706.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41565]
 gi|381315453|gb|EIC56216.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. 41566]
 gi|383799948|gb|AFH47030.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. B182]
 gi|392617222|gb|EIW99647.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. Levine 15]
 gi|392620794|gb|EIX03160.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. Levine 1]
 gi|392733879|gb|EIZ91070.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21539]
 gi|392738743|gb|EIZ95883.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35199]
 gi|392741709|gb|EIZ98805.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35185]
 gi|392752921|gb|EJA09861.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 33953]
 gi|392755522|gb|EJA12431.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35188]
 gi|392757357|gb|EJA14247.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21559]
 gi|392761715|gb|EJA18534.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19449]
 gi|392762301|gb|EJA19116.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19447]
 gi|392768964|gb|EJA25710.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19567]
 gi|392779346|gb|EJA36015.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 35202]
 gi|392781535|gb|EJA38176.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22513]
 gi|392783044|gb|EJA39674.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21550]
 gi|392786165|gb|EJA42722.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22425]
 gi|392786615|gb|EJA43171.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21538]
 gi|392799178|gb|EJA55437.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM N1543]
 gi|392800361|gb|EJA56599.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM N18486]
 gi|392804608|gb|EJA60761.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 22462]
 gi|392806935|gb|EJA63019.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 21554]
 gi|392809412|gb|EJA65449.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19443]
 gi|392820345|gb|EJA76195.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19593]
 gi|392823890|gb|EJA79681.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 37978]
 gi|392834164|gb|EJA89774.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19536]
 gi|392834827|gb|EJA90429.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 19470]
 gi|392836033|gb|EJA91621.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Newport str. CVM 4176]
 gi|395981367|gb|EJH90589.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 622731-39]
 gi|395982020|gb|EJH91241.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 640631]
 gi|395988035|gb|EJH97197.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639016-6]
 gi|395994465|gb|EJI03541.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-0424]
 gi|395995843|gb|EJI04907.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 485549-17]
 gi|396009353|gb|EJI18286.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629164-26]
 gi|396017172|gb|EJI26038.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 596866-70]
 gi|396018377|gb|EJI27239.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 596866-22]
 gi|396022061|gb|EJI30875.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639672-46]
 gi|396027772|gb|EJI36535.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629164-37]
 gi|396028055|gb|EJI36817.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 639672-50]
 gi|396034765|gb|EJI43446.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-1427]
 gi|396042503|gb|EJI51125.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 77-2659]
 gi|396044051|gb|EJI52649.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 78-1757]
 gi|396048687|gb|EJI57236.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22510-1]
 gi|396055888|gb|EJI64364.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648905 5-18]
 gi|396068034|gb|EJI76382.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 6-18]
 gi|396069674|gb|EJI78012.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 50-3079]
 gi|396070813|gb|EJI79141.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 58-6482]
 gi|402515169|gb|EJW22584.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00322]
 gi|402516957|gb|EJW24365.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00325]
 gi|402521782|gb|EJW29116.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00326]
 gi|402532349|gb|EJW39546.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Heidelberg str. CFSAN00328]
 gi|414014885|gb|EKS98719.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm1]
 gi|414016082|gb|EKS99872.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm8]
 gi|414016252|gb|EKT00026.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm2]
 gi|414029128|gb|EKT12290.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm9]
 gi|414030651|gb|EKT13744.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm3]
 gi|414033435|gb|EKT16386.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm4]
 gi|414043986|gb|EKT26449.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm6]
 gi|414044730|gb|EKT27166.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm10]
 gi|414049811|gb|EKT32010.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm11]
 gi|414057077|gb|EKT38844.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm12]
 gi|414063355|gb|EKT44505.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhimurium str. STm5]
 gi|434939815|gb|ELL46570.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Pullorum str. ATCC 9120]
 gi|434959903|gb|ELL53349.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CHS44]
 gi|434968231|gb|ELL60983.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1882]
 gi|434970710|gb|ELL63271.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1884]
 gi|434971444|gb|ELL63957.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE30663]
 gi|434974529|gb|ELL66884.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22704]
 gi|434980988|gb|ELL72875.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1594]
 gi|434984610|gb|ELL76350.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1566]
 gi|434985392|gb|ELL77079.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1580]
 gi|434992976|gb|ELL84415.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1543]
 gi|435000026|gb|ELL91200.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1441]
 gi|435005005|gb|ELL95927.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1810]
 gi|435005923|gb|ELL96843.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1558]
 gi|435012435|gb|ELM03110.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1018]
 gi|435019241|gb|ELM09685.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1010]
 gi|435023188|gb|ELM13484.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1729]
 gi|435029640|gb|ELM19698.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0895]
 gi|435033787|gb|ELM23679.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0899]
 gi|435033814|gb|ELM23704.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1457]
 gi|435035721|gb|ELM25566.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1747]
 gi|435045988|gb|ELM35614.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0968]
 gi|435046754|gb|ELM36369.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1444]
 gi|435058238|gb|ELM47593.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1445]
 gi|435065362|gb|ELM54468.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1565]
 gi|435067272|gb|ELM56333.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1808]
 gi|435068463|gb|ELM57491.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1559]
 gi|435076526|gb|ELM65309.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1811]
 gi|435083461|gb|ELM72062.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1455]
 gi|435084578|gb|ELM73163.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_0956]
 gi|435088202|gb|ELM76659.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1725]
 gi|435093190|gb|ELM81530.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1575]
 gi|435097440|gb|ELM85699.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1745]
 gi|435106611|gb|ELM94628.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 576709]
 gi|435107942|gb|ELM95925.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1791]
 gi|435108798|gb|ELM96763.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CDC_2010K_1795]
 gi|435119002|gb|ELN06653.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 635290-58]
 gi|435119068|gb|ELN06707.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-16]
 gi|435126930|gb|ELN14324.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-19]
 gi|435136584|gb|ELN23674.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607308-9]
 gi|435148450|gb|ELN35166.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE15-1]
 gi|435148862|gb|ELN35576.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_N202]
 gi|435158859|gb|ELN45231.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_56-3991]
 gi|435159922|gb|ELN46240.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_81-2490]
 gi|435161282|gb|ELN47524.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_76-3618]
 gi|435172174|gb|ELN57717.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SL909]
 gi|435172835|gb|ELN58360.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SL913]
 gi|435179253|gb|ELN64403.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CVM_69-4941]
 gi|435180522|gb|ELN65630.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 638970-15]
 gi|435192061|gb|ELN76617.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 17927]
 gi|435193613|gb|ELN78092.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. CHS4]
 gi|435202339|gb|ELN86193.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 22-17]
 gi|435210336|gb|ELN93607.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 40-18]
 gi|435214406|gb|ELN97206.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 13183-1]
 gi|435214439|gb|ELN97235.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 22558]
 gi|435218062|gb|ELO00469.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642044 4-1]
 gi|435218828|gb|ELO01229.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 561362 1-1]
 gi|435228671|gb|ELO10094.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642046 4-7]
 gi|435235014|gb|ELO15867.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648900 1-16]
 gi|435235812|gb|ELO16594.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648898 4-5]
 gi|435239116|gb|ELO19724.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648899 3-17]
 gi|435240922|gb|ELO21312.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 1-17]
 gi|435256849|gb|ELO36143.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648902 6-8]
 gi|435258314|gb|ELO37581.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 39-2]
 gi|435258807|gb|ELO38067.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648903 1-6]
 gi|435265142|gb|ELO44027.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 653049 13-19]
 gi|435271874|gb|ELO50312.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648904 3-6]
 gi|435272119|gb|ELO50540.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 642044 8-1]
 gi|435274171|gb|ELO52295.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 561362 9-7]
 gi|435289716|gb|ELO66666.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 648901 16-16]
 gi|435294683|gb|ELO71303.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 543463 42-20]
 gi|435298617|gb|ELO74826.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SARB17]
 gi|435309157|gb|ELO83938.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 76-2651]
 gi|435314072|gb|ELO87550.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 81-2625]
 gi|435314631|gb|ELO88028.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 50-5646]
 gi|435324572|gb|ELO96505.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 62-1976]
 gi|435327974|gb|ELO99625.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 53-407]
 gi|435335768|gb|ELP05906.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 6.0562-1]
 gi|436411184|gb|ELP09137.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH08SF124]
 gi|436411786|gb|ELP09734.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH10GFN094]
 gi|436414667|gb|ELP12594.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Agona str. SH11G1113]
 gi|444848870|gb|ELX73989.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. SL1438]
 gi|444855981|gb|ELX81019.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Dublin str. HWS51]
 gi|444863429|gb|ELX88254.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE8a]
 gi|444867784|gb|ELX92461.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. SE10]
 gi|444872192|gb|ELX96552.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 20037]
 gi|444877816|gb|ELY01951.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 18569]
 gi|444891018|gb|ELY14302.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 436]
 gi|451911971|gb|AGF83777.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Javiana str. CFSAN001992]
          Length = 615

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|238918478|ref|YP_002931992.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
            93-146]
 gi|238868046|gb|ACR67757.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
            93-146]
          Length = 611

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/608 (50%), Positives = 416/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 1060
            +   +  ++    +   E  +     S+       KF  +   ++K R A + EG +S  
Sbjct: 183  SELPEEELDDDGDENEDEDDDSDDDNSIDPELARQKFVELRQQYEKTRLAIKAEGRSSGK 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L   +R  +++V   E+ I+++ V +  MP+ +FI 
Sbjct: 243  AQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFIT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE ++ W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFTGNETSITWFDAALAMGKPWGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  RDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 407/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 270
           +   +  ++    +   E  +     S+       KF  +   ++K R A + EG +S  
Sbjct: 183 SELPEEELDDDGDENEDEDDDSDDDNSIDPELARQKFVELRQQYEKTRLAIKAEGRSSGK 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L   +R  +++V   E+ I+++ V +  MP+ +FI 
Sbjct: 243 AQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFIT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE ++ W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFTGNETSITWFDAALAMGKPWGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|304312382|ref|YP_003811980.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
            proteobacterium HdN1]
 gi|301798115|emb|CBL46337.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32) [gamma
            proteobacterium HdN1]
          Length = 627

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/621 (48%), Positives = 415/621 (66%), Gaps = 16/621 (2%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            + E  + + K LI  GKE+G+LTF+++ND LP DI D E +E II     M I V E   
Sbjct: 3    DTEQQKSQLKQLIARGKEQGFLTFADVNDHLPPDITDPEQVEDIIAMINDMGIPVHEAAP 62

Query: 885  DTETLMLSNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
              E L+      S++D  +    A + +D++ GRT DP++MYMREMGSVELLTR+GEI I
Sbjct: 63   GAEGLLRGGANPSNEDASDEESPANAVIDAEPGRTTDPVRMYMREMGSVELLTREGEIVI 122

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFS 995
            AKRIEEG+++++ A++  P  +  +L    K+   E ++++I+ G +D         +F 
Sbjct: 123  AKRIEEGIREVMSALAFWPDAVDVVLDEYSKVDSQERRLNDIISGYLDLAECEVEESDFQ 182

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMR 1048
            +N    +    + +     E   ++  +    + +        E+ ++F  +    +  +
Sbjct: 183  ANAPAKEATLKDKDLSDDDEEEESEGESGDSSEEEDAGSLDPEEARVRFGALLDALNAAK 242

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
               E++G  S+ +  A   ++N+ +  +   +  E+L   +R  + +V + E+ I+   +
Sbjct: 243  TTREEKGRKSKPFTNAQEELANQFITFKLVPRLFEQLVGGVRETLERVRENERAIMTRCI 302

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
                MPR  F+K FP NE N+ WVD     +  Y   +      I +LQQ L+ L++ + 
Sbjct: 303  RIAKMPRKDFVKQFPGNETNIEWVDKIAGGKTAYAERVGALKDDIIKLQQNLLGLESTLS 362

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L + ++++INR++  GE KA +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 363  LSIAEIKEINRRISIGEAKAARAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQ
Sbjct: 423  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQ 482

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP P  +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P 
Sbjct: 483  EMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTMQSPV 542

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            DAA   S+R   +D+L SLT RE+KVL MRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 543  DAATAESLREATRDVLASLTAREAKVLAMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 602

Query: 1409 KALRKLRHPSRYYKLKIFLEG 1429
            KALRKLRHPSR   L+ FL+G
Sbjct: 603  KALRKLRHPSRSEHLRSFLDG 623



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 294/607 (48%), Positives = 405/607 (66%), Gaps = 16/607 (2%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           + E  + + K LI  GKE+G+LTF+++ND LP DI D E +E II     M I V E   
Sbjct: 3   DTEQQKSQLKQLIARGKEQGFLTFADVNDHLPPDITDPEQVEDIIAMINDMGIPVHEAAP 62

Query: 95  DTETLMLSNIT-SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
             E L+      S++D  +    A + +D++ GRT DP++MYMREMGSVELLTR+GEI I
Sbjct: 63  GAEGLLRGGANPSNEDASDEESPANAVIDAEPGRTTDPVRMYMREMGSVELLTREGEIVI 122

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFS 205
           AKRIEEG+++++ A++  P  +  +L    K+   E ++++I+ G +D         +F 
Sbjct: 123 AKRIEEGIREVMSALAFWPDAVDVVLDEYSKVDSQERRLNDIISGYLDLAECEVEESDFQ 182

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMR 258
           +N    +    + +     E   ++  +    + +        E+ ++F  +    +  +
Sbjct: 183 ANAPAKEATLKDKDLSDDDEEEESEGESGDSSEEEDAGSLDPEEARVRFGALLDALNAAK 242

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
              E++G  S+ +  A   ++N+ +  +   +  E+L   +R  + +V + E+ I+   +
Sbjct: 243 TTREEKGRKSKPFTNAQEELANQFITFKLVPRLFEQLVGGVRETLERVRENERAIMTRCI 302

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
               MPR  F+K FP NE N+ WVD     +  Y   +      I +LQQ L+ L++ + 
Sbjct: 303 RIAKMPRKDFVKQFPGNETNIEWVDKIAGGKTAYAERVGALKDDIIKLQQNLLGLESTLS 362

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L + ++++INR++  GE KA +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 363 LSIAEIKEINRRISIGEAKAARAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQ
Sbjct: 423 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQ 482

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP P  +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P 
Sbjct: 483 EMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTMQSPV 542

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           DAA   S+R   +D+L SLT RE+KVL MRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 543 DAATAESLREATRDVLASLTAREAKVLAMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 602

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 603 KALRKLR 609


>gi|261344812|ref|ZP_05972456.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
 gi|282567259|gb|EFB72794.1| RNA polymerase sigma factor RpoD [Providencia rustigianii DSM 4541]
          Length = 616

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 311/613 (50%), Positives = 422/613 (68%), Gaps = 11/613 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 997
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 998  --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
              + + +   NN+EE+   E S    + +        +  KFS++   ++K R   ++ G
Sbjct: 183  VGSELPQEELNNDEEEEEDEDSEDSDTDDDNSIDPELARQKFSDLREQYEKTRSHIKQYG 242

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +    + A N +S+     R   K  + L + +R  + +V Q E+ I+++ V +C MP+
Sbjct: 243  RSDAKTVAAINQLSDVFKEFRLVPKQFDYLVNNMREMMERVRQQERTIMKLCVEQCKMPK 302

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +FI +F  NE +  W+     +   ++  L      +    Q+L  ++ +  L +  ++
Sbjct: 303  KNFITLFGGNETSETWLTAAKAMNKPWSEKLLDVEEDVLRCLQRLRQIEEETGLTIEQVK 362

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 483  PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 542

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543  LRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 603  HPSRSEVLRSFLD 615



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/600 (50%), Positives = 413/600 (68%), Gaps = 11/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 207
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 208 --NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
             + + +   NN+EE+   E S    + +        +  KFS++   ++K R   ++ G
Sbjct: 183 VGSELPQEELNNDEEEEEDEDSEDSDTDDDNSIDPELARQKFSDLREQYEKTRSHIKQYG 242

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +    + A N +S+     R   K  + L + +R  + +V Q E+ I+++ V +C MP+
Sbjct: 243 RSDAKTVAAINQLSDVFKEFRLVPKQFDYLVNNMREMMERVRQQERTIMKLCVEQCKMPK 302

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +FI +F  NE +  W+     +   ++  L      +    Q+L  ++ +  L +  ++
Sbjct: 303 KNFITLFGGNETSETWLTAAKAMNKPWSEKLLDVEEDVLRCLQRLRQIEEETGLTIEQVK 362

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 483 PEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 542

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 LRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|352080473|ref|ZP_08951412.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodanobacter sp. 2APBS1]
 gi|389796951|ref|ZP_10199997.1| RNA polymerase sigma factor RpoD [Rhodanobacter sp. 116-2]
 gi|351683754|gb|EHA66830.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodanobacter sp. 2APBS1]
 gi|388448044|gb|EIM04035.1| RNA polymerase sigma factor RpoD [Rhodanobacter sp. 116-2]
          Length = 625

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 319/620 (51%), Positives = 415/620 (66%), Gaps = 31/620 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+ L  
Sbjct: 12   EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDPLAD 71

Query: 892  SNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
               +S DD   A EA   LS VDS+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 72   KAGSSTDDEAAAEEAVALLSAVDSEVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 131

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            GL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       K    
Sbjct: 132  GLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAAD----LARKEKEA 187

Query: 1010 EKILIESSSADL--------------------STEQLEKLKYESLIKFSNISFHFDKMRK 1049
              +L                            S    E++K     +   +  H+ K +K
Sbjct: 188  AALLAPEPEVGDDDADTDDDDTATEDEEEAGPSGPDPEEVKR----RMELLREHYAKFQK 243

Query: 1050 AFEKEGYNSESYI-KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
            A  K    ++  I K  + ++ E L ++  +  I+     LR  +N +   E+ +++I V
Sbjct: 244  AAPKAASITDRKIVKLRDLMAEEFLKLKLPSALIDGFVRKLREVVNDIRHHERVLMDIFV 303

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
             +  MP+  FIK FP NE NL WV   ++ +  ++  +  +  +I   Q+KL  ++  + 
Sbjct: 304  KQVKMPKAEFIKAFPSNEGNLEWVAELSRKRQKWSPNIKVHREAIDAEQEKLAAIERKLF 363

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            LPL D++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 364  LPLIDIKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 423

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 424  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 483

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            + G E  P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P 
Sbjct: 484  QFGREATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPI 543

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A    +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 544  DSATETGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 603

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR  +L+ FL+
Sbjct: 604  KALRKLRHPSRSEQLRSFLD 623



 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 405/607 (66%), Gaps = 31/607 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+ L  
Sbjct: 12  EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDPLAD 71

Query: 102 SNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
              +S DD   A EA   LS VDS+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 72  KAGSSTDDEAAAEEAVALLSAVDSEVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 131

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           GL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       K    
Sbjct: 132 GLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAAD----LARKEKEA 187

Query: 220 EKILIESSSADL--------------------STEQLEKLKYESLIKFSNISFHFDKMRK 259
             +L                            S    E++K     +   +  H+ K +K
Sbjct: 188 AALLAPEPEVGDDDADTDDDDTATEDEEEAGPSGPDPEEVKR----RMELLREHYAKFQK 243

Query: 260 AFEKEGYNSESYI-KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
           A  K    ++  I K  + ++ E L ++  +  I+     LR  +N +   E+ +++I V
Sbjct: 244 AAPKAASITDRKIVKLRDLMAEEFLKLKLPSALIDGFVRKLREVVNDIRHHERVLMDIFV 303

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
            +  MP+  FIK FP NE NL WV   ++ +  ++  +  +  +I   Q+KL  ++  + 
Sbjct: 304 KQVKMPKAEFIKAFPSNEGNLEWVAELSRKRQKWSPNIKVHREAIDAEQEKLAAIERKLF 363

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           LPL D++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 364 LPLIDIKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 423

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 424 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 483

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           + G E  P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P 
Sbjct: 484 QFGREATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPI 543

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A    +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 544 DSATETGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 603

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 604 KALRKLR 610


>gi|409395491|ref|ZP_11246561.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Chol1]
 gi|409395588|ref|ZP_11246652.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Chol1]
 gi|409119790|gb|EKM96164.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Chol1]
 gi|409119873|gb|EKM96245.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. Chol1]
          Length = 618

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 311/613 (50%), Positives = 422/613 (68%), Gaps = 21/613 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +                E 
Sbjct: 130  REVMSAIAHFPGTVDGILADYERVTNEGGRLSDILSGYIDPDDDG-----AAGAPQEVEP 184

Query: 1012 ILIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEG 1055
            +  + ++  ++ ++ +  + E                +  +F  ++   +K +KA +K G
Sbjct: 185  VAPQVAAKPVADDKDDDEEEESDSEEEEGDGGPDPEVARARFGAVAEQLEKAKKALKKHG 244

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
              S+  I     ++   + I+   K  + L + +R+ +NQ+   E+ ++++ V    MPR
Sbjct: 245  RASQQAIDELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAVMQLCVRDARMPR 304

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              F++ FP NE NL W +     +  Y   +      I+  QQKLI L+ +  L + D++
Sbjct: 305  ADFLRQFPSNETNLAWAEELAAGKSKYAEAIGARKEDIRRCQQKLIELEQECELAIADIK 364

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 425  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 484

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S
Sbjct: 485  PEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVES 544

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545  LKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604

Query: 1416 HPSRYYKLKIFLE 1428
            HP+R   L+ FL+
Sbjct: 605  HPTRSEHLRSFLD 617



 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/600 (50%), Positives = 413/600 (68%), Gaps = 21/600 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +                E 
Sbjct: 130 REVMSAIAHFPGTVDGILADYERVTNEGGRLSDILSGYIDPDDDG-----AAGAPQEVEP 184

Query: 222 ILIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEG 265
           +  + ++  ++ ++ +  + E                +  +F  ++   +K +KA +K G
Sbjct: 185 VAPQVAAKPVADDKDDDEEEESDSEEEEGDGGPDPEVARARFGAVAEQLEKAKKALKKHG 244

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
             S+  I     ++   + I+   K  + L + +R+ +NQ+   E+ ++++ V    MPR
Sbjct: 245 RASQQAIDELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAVMQLCVRDARMPR 304

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             F++ FP NE NL W +     +  Y   +      I+  QQKLI L+ +  L + D++
Sbjct: 305 ADFLRQFPSNETNLAWAEELAAGKSKYAEAIGARKEDIRRCQQKLIELEQECELAIADIK 364

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 425 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 484

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S
Sbjct: 485 PEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVES 544

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 LKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|448236296|ref|YP_001573337.2| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. arizonae
            serovar 62:z4,z23:- str. RSK2980]
          Length = 615

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|289827081|ref|ZP_06545870.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Typhi str. E98-3139]
          Length = 615

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFIMLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFIMLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|374314300|ref|YP_005060729.1| RNA polymerase major s factor [Serratia symbiotica str. 'Cinara
            cedri']
 gi|363988526|gb|AEW44717.1| RNA polymerase major s factor [Serratia symbiotica str. 'Cinara
            cedri']
          Length = 627

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 312/617 (50%), Positives = 425/617 (68%), Gaps = 30/617 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25   QNPQSQLKLLVTHGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 84

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + LML+  T+D D E+A EAA   LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+I
Sbjct: 85   DDLMLAENTNDTD-EDAVEAATQVLSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDI 143

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D +          
Sbjct: 144  AKRIEDGINQVQCSVAEYPEAITYLLEQYDRVDAGEARMSDLITGFVDPD---------- 193

Query: 1004 NKNNNEEKIL--IESSSADLSTEQL---EKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
                 EE I+  +    ++LSTE+    ++ + ++ I        F  +R  +E      
Sbjct: 194  ----AEEDIIPTVTHIGSELSTEEQNEDDEAEDDNSIDPELARQKFADLRNQYEVTRLVI 249

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H N + E+L +       R   K  + + +++R+ ++++   E+ I++  V +C
Sbjct: 250  IENSRSHANATQEILKLSEVFKQFRLVPKQFDFVVNSMRSMMDRIRAQERIIMKRCVEQC 309

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W  N  ++   ++  L      ++   QKL  ++ +  L +
Sbjct: 310  KMPKKNFVSLFAGNESSDTWFKNAQEMVKPWSEKLKDVTEDVQCSLQKLREIEEETGLTI 369

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 370  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 429

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 430  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 489

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M M E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 490  REPMPEELAARMLMSEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 549

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 550  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 609

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 610  RKLRHPSRSEVLRSFLD 626



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 416/604 (68%), Gaps = 30/604 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25  QNPQSQLKLLVTHGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 84

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + LML+  T+D D E+A EAA   LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+I
Sbjct: 85  DDLMLAENTNDTD-EDAVEAATQVLSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDI 143

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D +          
Sbjct: 144 AKRIEDGINQVQCSVAEYPEAITYLLEQYDRVDAGEARMSDLITGFVDPD---------- 193

Query: 214 NKNNNEEKIL--IESSSADLSTEQL---EKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
                EE I+  +    ++LSTE+    ++ + ++ I        F  +R  +E      
Sbjct: 194 ----AEEDIIPTVTHIGSELSTEEQNEDDEAEDDNSIDPELARQKFADLRNQYEVTRLVI 249

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H N + E+L +       R   K  + + +++R+ ++++   E+ I++  V +C
Sbjct: 250 IENSRSHANATQEILKLSEVFKQFRLVPKQFDFVVNSMRSMMDRIRAQERIIMKRCVEQC 309

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W  N  ++   ++  L      ++   QKL  ++ +  L +
Sbjct: 310 KMPKKNFVSLFAGNESSDTWFKNAQEMVKPWSEKLKDVTEDVQCSLQKLREIEEETGLTI 369

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 370 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 429

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 430 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 489

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M M E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 490 REPMPEELAARMLMSEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 549

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 550 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 609

Query: 622 RKLR 625
           RKLR
Sbjct: 610 RKLR 613


>gi|387126241|ref|YP_006294846.1| RNA polymerase sigma factor RpoD [Methylophaga sp. JAM1]
 gi|386273303|gb|AFI83201.1| RNA polymerase sigma factor RpoD [Methylophaga sp. JAM1]
          Length = 612

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/609 (49%), Positives = 425/609 (69%), Gaps = 6/609 (0%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1    MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 886  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            T+ +  +   ++S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61   TDEMERLAEAVSSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRV 1000
            IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G +  ++  +S++  
Sbjct: 121  IAKRIEAGLRESLLMLSTYPPVISSFLEFYDAVEAGEMRLNELIRGFVAPEELVASDDDD 180

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE-GYNSE 1059
                 +++ +    +    D      +       I        F  +++A++       +
Sbjct: 181  DDVTSSSDSDDSDSDDDDDDDVDGVSDDEDDSGEIDPEEARARFTALKEAYKNVLATEGD 240

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            + I++    SN  +  + T K++  L   +   I +V + EK I++IVV + GM R  FI
Sbjct: 241  AMIESREQASNLFMEFKLTPKTLLYLNGLMAETIAEVRKQEKIIMDIVVEQAGMNRRDFI 300

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
              F  NE NL W D   + +  Y+  + +N+  I   Q KL  +  D  L ++++++I+R
Sbjct: 301  DAFQGNESNLEWSDKFIRAKKHYSSTIKKNLDDILAAQSKLAEIAEDRGLDISEIKEISR 360

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+R
Sbjct: 361  QMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 420

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP P  +
Sbjct: 421  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREPTPDEL 480

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P+D+A+   +R  
Sbjct: 481  AERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDINVMSPADSAIIEGLREA 540

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 541  TQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 600

Query: 1420 YYKLKIFLE 1428
              +L+ FL+
Sbjct: 601  SDQLRSFLD 609



 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 299/604 (49%), Positives = 418/604 (69%), Gaps = 7/604 (1%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1   MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 96  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           T+ +  +   ++S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61  TDEMERLAEAVSSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRV 210
           IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G +  ++  +S++  
Sbjct: 121 IAKRIEAGLRESLLMLSTYPPVISSFLEFYDAVEAGEMRLNELIRGFVAPEELVASDDDD 180

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE-GYNSE 269
                +++ +    +    D      +       I        F  +++A++       +
Sbjct: 181 DDVTSSSDSDDSDSDDDDDDDVDGVSDDEDDSGEIDPEEARARFTALKEAYKNVLATEGD 240

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           + I++    SN  +  + T K++  L   +   I +V + EK I++IVV + GM R  FI
Sbjct: 241 AMIESREQASNLFMEFKLTPKTLLYLNGLMAETIAEVRKQEKIIMDIVVEQAGMNRRDFI 300

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
             F  NE NL W D   + +  Y+  + +N+  I   Q KL  +  D  L ++++++I+R
Sbjct: 301 DAFQGNESNLEWSDKFIRAKKHYSSTIKKNLDDILAAQSKLAEIAEDRGLDISEIKEISR 360

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+R
Sbjct: 361 QMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 420

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP P  +
Sbjct: 421 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREPTPDEL 480

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P+D+A+   +R  
Sbjct: 481 AERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDINVMSPADSAIIEGLREA 540

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLA 628
            + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P  
Sbjct: 541 TQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 600

Query: 629 HDWL 632
            D L
Sbjct: 601 SDQL 604


>gi|383816574|ref|ZP_09971969.1| RNA polymerase sigma factor RpoD [Serratia sp. M24T3]
 gi|383294568|gb|EIC82907.1| RNA polymerase sigma factor RpoD [Serratia sp. M24T3]
          Length = 612

 Score =  589 bits (1519), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/609 (50%), Positives = 415/609 (68%), Gaps = 7/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTF+E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+    D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENRPDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 1000
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEEIAPTATH 182

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 1059
            +    +N E     +    D   E    +  E +  KF+ +    +  R   +K G + +
Sbjct: 183  VGSELSNEELDDSDDDEDEDDDAEDDNSIDPELARQKFTELREQHEATRSVIKKNGRSHK 242

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            S  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+
Sbjct: 243  SSAEEILKLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKLCVEQCKMPKKNFV 302

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
             +F  NE N  W +    +   ++  L      ++   QKL  ++ +  L +  ++DINR
Sbjct: 303  NLFAGNETNQTWFEAALAMAKPWSEKLKEVTEDVQRGLQKLRQIEEETGLTIEQVKDINR 362

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483  AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 543  THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 602

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 603  SEVLRSFLD 611



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/596 (50%), Positives = 406/596 (68%), Gaps = 7/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTF+E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+    D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENRPDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 210
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEEIAPTATH 182

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 269
           +    +N E     +    D   E    +  E +  KF+ +    +  R   +K G + +
Sbjct: 183 VGSELSNEELDDSDDDEDEDDDAEDDNSIDPELARQKFTELREQHEATRSVIKKNGRSHK 242

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           S  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+
Sbjct: 243 SSAEEILKLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKLCVEQCKMPKKNFV 302

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
            +F  NE N  W +    +   ++  L      ++   QKL  ++ +  L +  ++DINR
Sbjct: 303 NLFAGNETNQTWFEAALAMAKPWSEKLKEVTEDVQRGLQKLRQIEEETGLTIEQVKDINR 362

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483 AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|269137812|ref|YP_003294512.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Edwardsiella tarda EIB202]
 gi|387866554|ref|YP_005698023.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda FL6-60]
 gi|267983472|gb|ACY83301.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Edwardsiella tarda EIB202]
 gi|304557867|gb|ADM40531.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda FL6-60]
          Length = 611

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/608 (50%), Positives = 416/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 1060
            +   +  ++    +   E  +     S+       KF  +   ++K R A + EG +S  
Sbjct: 183  SELPEEELDDDEDEDEDEDDDSDDDNSIDPELARQKFVELREQYEKTRLAIKAEGRSSGK 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L   +R  +++V   E+ I+++ V +  MP+ +FI 
Sbjct: 243  AQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFIT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE ++ W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFTGNETSITWFDAALAMGKPWGEKLKDMREDVERSLQKLHQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  RDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 407/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNSES 270
           +   +  ++    +   E  +     S+       KF  +   ++K R A + EG +S  
Sbjct: 183 SELPEEELDDDEDEDEDEDDDSDDDNSIDPELARQKFVELREQYEKTRLAIKAEGRSSGK 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L   +R  +++V   E+ I+++ V +  MP+ +FI 
Sbjct: 243 AQEEIQNLSEIFKQFRLVPKQFDYLVSNMREMMDRVRGQERLIMKLCVEQSKMPKKNFIT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE ++ W D    +   +   L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFTGNETSITWFDAALAMGKPWGEKLKDMREDVERSLQKLHQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|416426595|ref|ZP_11693090.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 315996572]
 gi|416429169|ref|ZP_11694382.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-1]
 gi|416439221|ref|ZP_11700098.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-3]
 gi|416445946|ref|ZP_11704701.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-4]
 gi|416451337|ref|ZP_11708087.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 515920-1]
 gi|416460084|ref|ZP_11714529.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 515920-2]
 gi|416462592|ref|ZP_11715559.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 531954]
 gi|416480236|ref|ZP_11722753.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. NC_MB110209-0054]
 gi|416492812|ref|ZP_11727599.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. OH_2009072675]
 gi|416500790|ref|ZP_11731652.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CASC_09SCPH15965]
 gi|416546667|ref|ZP_11754061.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 19N]
 gi|416577596|ref|ZP_11769882.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 81038-01]
 gi|416584126|ref|ZP_11773866.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MD_MDA09249507]
 gi|416591539|ref|ZP_11778483.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 414877]
 gi|416598414|ref|ZP_11782801.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 366867]
 gi|416606930|ref|ZP_11788171.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 413180]
 gi|416610473|ref|ZP_11790080.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 446600]
 gi|416619019|ref|ZP_11794825.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 609458-1]
 gi|416628553|ref|ZP_11799718.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 556150-1]
 gi|416641696|ref|ZP_11805515.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 609460]
 gi|416647002|ref|ZP_11808001.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 507440-20]
 gi|416656894|ref|ZP_11813350.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 556152]
 gi|416670369|ref|ZP_11820083.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB101509-0077]
 gi|416675221|ref|ZP_11821544.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB102109-0047]
 gi|416699973|ref|ZP_11828987.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB110209-0055]
 gi|416705892|ref|ZP_11831151.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB111609-0052]
 gi|416712428|ref|ZP_11836139.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 2009083312]
 gi|416718626|ref|ZP_11840734.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 2009085258]
 gi|416723019|ref|ZP_11843784.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 315731156]
 gi|416733008|ref|ZP_11850099.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2009159199]
 gi|416737738|ref|ZP_11852891.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008282]
 gi|416748459|ref|ZP_11858716.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008283]
 gi|416754851|ref|ZP_11861643.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008284]
 gi|416761493|ref|ZP_11865544.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008285]
 gi|416771380|ref|ZP_11872645.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008287]
 gi|418481711|ref|ZP_13050734.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 80959-06]
 gi|418490894|ref|ZP_13057428.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035278]
 gi|418495693|ref|ZP_13062131.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035318]
 gi|418498510|ref|ZP_13064924.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035320]
 gi|418505718|ref|ZP_13072064.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035321]
 gi|418507681|ref|ZP_13074000.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035327]
 gi|418524470|ref|ZP_13090455.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008286]
 gi|322613615|gb|EFY10556.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 315996572]
 gi|322621208|gb|EFY18066.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-1]
 gi|322624271|gb|EFY21105.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-3]
 gi|322627991|gb|EFY24780.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 495297-4]
 gi|322633109|gb|EFY29851.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 515920-1]
 gi|322636314|gb|EFY33022.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 515920-2]
 gi|322643488|gb|EFY40050.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 531954]
 gi|322644793|gb|EFY41328.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. NC_MB110209-0054]
 gi|322648602|gb|EFY45049.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. OH_2009072675]
 gi|322653654|gb|EFY49980.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CASC_09SCPH15965]
 gi|322657762|gb|EFY54030.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 19N]
 gi|322663863|gb|EFY60062.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 81038-01]
 gi|322669126|gb|EFY65277.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MD_MDA09249507]
 gi|322672881|gb|EFY68988.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 414877]
 gi|322678129|gb|EFY74192.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 366867]
 gi|322681305|gb|EFY77338.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 413180]
 gi|322687765|gb|EFY83732.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 446600]
 gi|323195577|gb|EFZ80754.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 609458-1]
 gi|323199742|gb|EFZ84832.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 556150-1]
 gi|323202510|gb|EFZ87550.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 609460]
 gi|323212446|gb|EFZ97263.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 556152]
 gi|323215072|gb|EFZ99820.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB101509-0077]
 gi|323222802|gb|EGA07167.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB102109-0047]
 gi|323224117|gb|EGA08410.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB110209-0055]
 gi|323230441|gb|EGA14559.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. MB111609-0052]
 gi|323235207|gb|EGA19293.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 2009083312]
 gi|323239248|gb|EGA23298.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 2009085258]
 gi|323244394|gb|EGA28400.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 315731156]
 gi|323247011|gb|EGA30977.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2009159199]
 gi|323253507|gb|EGA37336.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008282]
 gi|323256187|gb|EGA39923.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008283]
 gi|323262637|gb|EGA46193.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008284]
 gi|323267267|gb|EGA50751.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008285]
 gi|323269331|gb|EGA52786.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008287]
 gi|366058209|gb|EHN22498.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035318]
 gi|366064257|gb|EHN28457.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035278]
 gi|366064444|gb|EHN28641.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 80959-06]
 gi|366068025|gb|EHN32173.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035321]
 gi|366073262|gb|EHN37335.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035320]
 gi|366080935|gb|EHN44889.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. CT_02035327]
 gi|366830445|gb|EHN57315.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. 507440-20]
 gi|372207329|gb|EHP20828.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Montevideo str. IA_2010008286]
          Length = 615

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVSEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVSEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|392422733|ref|YP_006459337.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri CCUG 29243]
 gi|390984921|gb|AFM34914.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri CCUG 29243]
          Length = 617

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/607 (51%), Positives = 423/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130  REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAGPQEVEPETPQTT 189

Query: 1010 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             K   +    +   +   + +          + ++F  ++   +K +KA +K G  S+  
Sbjct: 190  AKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKALKKHGRASQQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            ++    ++   + I+   K  + L + +RN ++Q+   E+ I+++ V    MPR  F++ 
Sbjct: 250  VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE NL+W +     +  Y   +      I   QQKLI L+ +  L + D++DINR+M
Sbjct: 310  FPNNETNLDWAEQLASGKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADIKDINRRM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 550  EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/594 (51%), Positives = 414/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSSNNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +   ++  + ++       
Sbjct: 130 REVMSAIAHFPGTVDSILADYERVTTEGGRLSDILSGYIDPDDDGAAGPQEVEPETPQTT 189

Query: 220 EKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            K   +    +   +   + +          + ++F  ++   +K +KA +K G  S+  
Sbjct: 190 AKPAADDKDDEEEDDSDSEEEEGDGGPDPEVARMRFGAVAEQLEKAKKALKKHGRASQQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           ++    ++   + I+   K  + L + +RN ++Q+   E+ I+++ V    MPR  F++ 
Sbjct: 250 VEELEALAILFMPIKLVPKQYDALVERVRNALSQIRAQERAIMQLCVRDARMPRADFLRQ 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE NL+W +     +  Y   +      I   QQKLI L+ +  L + D++DINR+M
Sbjct: 310 FPNNETNLDWAEQLASGKGKYAEAIGNRKEDIVRCQQKLIELEQECDLVIADIKDINRRM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +
Sbjct: 490 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEATR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|23428541|gb|AAL11450.1| RNA polymerase sigma-70 subunit [Serratia plymuthica]
          Length = 612

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 420/610 (68%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E     ++   +   +  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182  HVGSELSTEEQNDDEEDEEDDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242  ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302  VTLFAGNETSDSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI++GNIGLMKAVDKFEYR
Sbjct: 362  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIRKGNIGLMKAVDKFEYR 421

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV RERIRQIEAKALRKLRHPS
Sbjct: 542  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVIRERIRQIEAKALRKLRHPS 601

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 602  RSEVLRSFLD 611



 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 411/597 (68%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  + ++D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENSNSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E     ++   +   +  +     S+       KF+++   ++  R   +K G + 
Sbjct: 182 HVGSELSTEEQNDDEEDEEDDDDAEDDNSIDPELARQKFTDLRDQYEATRLVIKKNGRSH 241

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242 ASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE + +W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302 VTLFAGNETSDSWFEAALAMAKPWSEKLKDVTDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI++GNIGLMKAVDKFEYR
Sbjct: 362 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIRKGNIGLMKAVDKFEYR 421

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV RERIRQIEAKALRKLR
Sbjct: 542 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVIRERIRQIEAKALRKLR 598


>gi|205354126|ref|YP_002227927.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Gallinarum str. 287/91]
 gi|205273907|emb|CAR38909.1| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica
            serovar Gallinarum str. 287/91]
          Length = 615

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 307/626 (49%), Positives = 414/626 (66%), Gaps = 38/626 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISF 1042
                EE++   ++       Q +    E                         KF+ +  
Sbjct: 172  ---AEEEMAPTATHVGYELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRA 228

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             +   R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ 
Sbjct: 229  QYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERL 288

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            I+++ V +C MP+ +FI +F  NE +  W +    +   ++  L      ++   QKL  
Sbjct: 289  IMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQ 348

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 349  IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 408

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 409  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 468

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 469  SRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDT 528

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
             +  P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRER
Sbjct: 529  TLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 588

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLE 1428
            IRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  IRQIEAKALRKLRHPSRSEVLRSFLD 614



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/613 (48%), Positives = 405/613 (66%), Gaps = 38/613 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPN----------- 171

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISF 252
               EE++   ++       Q +    E                         KF+ +  
Sbjct: 172 ---AEEEMAPTATHVGYELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRA 228

Query: 253 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            +   R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ 
Sbjct: 229 QYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERL 288

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
           I+++ V +C MP+ +FI +F  NE +  W +    +   ++  L      ++   QKL  
Sbjct: 289 IMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQ 348

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
           ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 349 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 408

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 409 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 468

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 469 SRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMEAPIGDDEDSHLGDFIEDT 528

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
            +  P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRER
Sbjct: 529 TLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 588

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 589 IRQIEAKALRKLR 601


>gi|270158971|ref|ZP_06187627.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|289166186|ref|YP_003456324.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
            NSW150]
 gi|269987310|gb|EEZ93565.1| RNA polymerase sigma factor RpoD [Legionella longbeachae D-4968]
 gi|288859359|emb|CBJ13295.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella longbeachae
            NSW150]
          Length = 622

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 316/610 (51%), Positives = 416/610 (68%), Gaps = 22/610 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----KNFSSNNRVIKGNKNNNE 1009
            + +++  P T+  +L   ++ +  EI+++EI+ G  D        SS   ++  ++   E
Sbjct: 134  LKSLAHYPETVQLVLDDYERFNAQEIRLNEIISGFADVEDEIAPASSIGSMLDEDQQQEE 193

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE-------KEGYNSESYI 1062
            E +L   S  +    +   ++ +          +FD +R+ +E       + G       
Sbjct: 194  EILL---SDEEDEDGEGGMVEVDDGPNPEQAKIYFDDLRETYEAAIVALKEHGRTHAKTT 250

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            KA   +S   L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  F
Sbjct: 251  KALEIMSESFLKLKLTSRQVDRLTRHFRQLRNHIREHERGIMRLCIEKARIPRKLFIDTF 310

Query: 1123 PENEINLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            P  E +L W+ N    ++   L + R   N   I  +Q +L+  + +  L ++++++INR
Sbjct: 311  PGQETDLEWL-NTIIAKYSKKLDMNRIQENTEEILRIQSRLVAFELEYGLSISEIKEINR 369

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            KM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 370  KMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 429

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +
Sbjct: 430  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEEL 489

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A KME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R  
Sbjct: 490  AEKMELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREA 549

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              +IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 550  TLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 609

Query: 1420 YYKLKIFLEG 1429
              KL+ FLEG
Sbjct: 610  SEKLRSFLEG 619



 Score =  568 bits (1463), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/596 (51%), Positives = 405/596 (67%), Gaps = 22/596 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----KNFSSNNRVIKGNKNNNE 219
           + +++  P T+  +L   ++ +  EI+++EI+ G  D        SS   ++  ++   E
Sbjct: 134 LKSLAHYPETVQLVLDDYERFNAQEIRLNEIISGFADVEDEIAPASSIGSMLDEDQQQEE 193

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE-------KEGYNSESYI 272
           E +L   S  +    +   ++ +          +FD +R+ +E       + G       
Sbjct: 194 EILL---SDEEDEDGEGGMVEVDDGPNPEQAKIYFDDLRETYEAAIVALKEHGRTHAKTT 250

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           KA   +S   L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  F
Sbjct: 251 KALEIMSESFLKLKLTSRQVDRLTRHFRQLRNHIREHERGIMRLCIEKARIPRKLFIDTF 310

Query: 333 PENEINLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           P  E +L W+ N    ++   L + R   N   I  +Q +L+  + +  L ++++++INR
Sbjct: 311 PGQETDLEWL-NTIIAKYSKKLDMNRIQENTEEILRIQSRLVAFELEYGLSISEIKEINR 369

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           KM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 370 KMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 429

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +
Sbjct: 430 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEEL 489

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A KME+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R  
Sbjct: 490 AEKMELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREA 549

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +IL +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 TLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|365972142|ref|YP_004953703.1| RNA polymerase sigma factor rpoD [Enterobacter cloacae EcWSU1]
 gi|365751055|gb|AEW75282.1| RNA polymerase sigma factor rpoD [Enterobacter cloacae EcWSU1]
          Length = 633

 Score =  589 bits (1518), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 306/631 (48%), Positives = 421/631 (66%), Gaps = 30/631 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 12   IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 71

Query: 878  SVSEHVLDTETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
             V E   D + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELL
Sbjct: 72   QVMEEAPDADDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELL 131

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N  
Sbjct: 132  TREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAE 191

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKM 1047
             +      +  +   +  ++    +   +  +    +        +  KF+ +   ++  
Sbjct: 192  EDMAPTATHVGSELSQEEMDDDEDEDEEDADDDTADDDNSIDPELAREKFAELRTQYEVT 251

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ 
Sbjct: 252  RDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLC 311

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---------- 1157
            V +C MP+ +FI +F  NE +  W          +N  +  N P  ++L           
Sbjct: 312  VEQCKMPKKNFITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKEDVFRGL 361

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 362  QKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 421

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 422  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 481

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 482  KLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 541

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED  +  P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 542  FIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 601

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 602  VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 632



 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 299/618 (48%), Positives = 412/618 (66%), Gaps = 30/618 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 12  IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 71

Query: 88  SVSEHVLDTETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
            V E   D + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELL
Sbjct: 72  QVMEEAPDADDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELL 131

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N  
Sbjct: 132 TREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAE 191

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKM 257
            +      +  +   +  ++    +   +  +    +        +  KF+ +   ++  
Sbjct: 192 EDMAPTATHVGSELSQEEMDDDEDEDEEDADDDTADDDNSIDPELAREKFAELRTQYEVT 251

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           R   + +G +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ 
Sbjct: 252 RDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLC 311

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---------- 367
           V +C MP+ +FI +F  NE +  W          +N  +  N P  ++L           
Sbjct: 312 VEQCKMPKKNFITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKEDVFRGL 361

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 362 QKLHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 421

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 422 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 481

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 482 KLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 541

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED  +  P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 542 FIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 601

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 602 VTRERIRQIEAKALRKLR 619


>gi|421378722|ref|ZP_15828801.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607307-6]
 gi|421431095|ref|ZP_15880681.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 8b-1]
 gi|437141579|ref|ZP_20683263.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607307-2]
 gi|437153525|ref|ZP_20690631.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629163]
 gi|437808650|ref|ZP_20840355.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 33944]
 gi|445346257|ref|ZP_21418688.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 13-1]
 gi|445358516|ref|ZP_21422708.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. PT23]
 gi|395995057|gb|EJI04122.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607307-6]
 gi|396054921|gb|EJI63413.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 8b-1]
 gi|435127747|gb|ELN15107.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 607307-2]
 gi|435141276|gb|ELN28218.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 629163]
 gi|435300318|gb|ELO76413.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 33944]
 gi|444878227|gb|ELY02350.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. 13-1]
 gi|444886071|gb|ELY09840.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Enteritidis str. PT23]
          Length = 615

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 415/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183  VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAVIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 406/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS-NITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+ N TS D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G 
Sbjct: 183 VGSELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAVIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|290474860|ref|YP_003467740.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
            SS-2004]
 gi|289174173|emb|CBJ80960.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus bovienii
            SS-2004]
          Length = 616

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/613 (50%), Positives = 419/613 (68%), Gaps = 11/613 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGECRLSDLITGFVDPNAEEDLSPTATH 182

Query: 1005 KNNN--EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              +   + ++       D  +E     + ++ I        F ++R  +E    + +SY 
Sbjct: 183  IGSELPQAELDDSDDDDDEESEDDADSEDDNSIDPELARQKFQELRDQYETTRQSIKSYG 242

Query: 1063 KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            ++H N + E+L +       R   K  + L + +R+ +++V   E+QI+++ V  C MP+
Sbjct: 243  RSHPNTAAEILTLSEVFKQFRLIPKQFDYLVNNMRSMMDRVRLQERQIMKMCVELCKMPK 302

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +FI +F  NE    W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 303  KNFITLFSGNETTDTWFTAAKAMNKPWSDKLSEVEDDVMRSLQKLRQIEEETGLTIEQVK 362

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED  +  P D+A + S
Sbjct: 483  PEELAERMLMPEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDTTLELPLDSATSES 542

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543  LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 603  HPSRSEVLRSFLD 615



 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 303/600 (50%), Positives = 410/600 (68%), Gaps = 11/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGECRLSDLITGFVDPNAEEDLSPTATH 182

Query: 215 KNNN--EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             +   + ++       D  +E     + ++ I        F ++R  +E    + +SY 
Sbjct: 183 IGSELPQAELDDSDDDDDEESEDDADSEDDNSIDPELARQKFQELRDQYETTRQSIKSYG 242

Query: 273 KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           ++H N + E+L +       R   K  + L + +R+ +++V   E+QI+++ V  C MP+
Sbjct: 243 RSHPNTAAEILTLSEVFKQFRLIPKQFDYLVNNMRSMMDRVRLQERQIMKMCVELCKMPK 302

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +FI +F  NE    W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 303 KNFITLFSGNETTDTWFTAAKAMNKPWSDKLSEVEDDVMRSLQKLRQIEEETGLTIEQVK 362

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED  +  P D+A + S
Sbjct: 483 PEELAERMLMPEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDTTLELPLDSATSES 542

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|296104731|ref|YP_003614877.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
            ATCC 13047]
 gi|392980728|ref|YP_006479316.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp.
            dissolvens SDM]
 gi|295059190|gb|ADF63928.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
            ATCC 13047]
 gi|392326661|gb|AFM61614.1| RNA polymerase sigma factor RpoD [Enterobacter cloacae subsp.
            dissolvens SDM]
          Length = 615

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 301/612 (49%), Positives = 416/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183  VGSELSQEEMDDDEDEDEEESDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303  NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 294/599 (49%), Positives = 407/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183 VGSELSQEEMDDDEDEDEEESDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303 NFITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVHRGLQKLQQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|401678685|ref|ZP_10810644.1| RNA polymerase sigma-70 factor [Enterobacter sp. SST3]
 gi|400214112|gb|EJO45039.1| RNA polymerase sigma-70 factor [Enterobacter sp. SST3]
          Length = 615

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/622 (48%), Positives = 418/622 (67%), Gaps = 30/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183  VGSELSQEEMDDDEDEDEEESDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTD 1166
            +FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ +
Sbjct: 303  NFITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQIEEE 352

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 353  TGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 412

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 413  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 472

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 473  LQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 532

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 533  PLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 592

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 593  EAKALRKLRHPSRSEVLRSFLD 614



 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/609 (48%), Positives = 409/609 (67%), Gaps = 30/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +  +D+D EEA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G 
Sbjct: 183 VGSELSQEEMDDDEDEDEEESDDDSADDDNSIDPELAREKFAELRTQYEVTRDTIKAKGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +  +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTD 376
           +FI +F  NE +  W          +N  +  N P  ++L           QKL  ++ +
Sbjct: 303 NFITLFTGNETSETW----------FNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQIEEE 352

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 353 TGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 412

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 413 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 472

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 473 LQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 532

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 533 PLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 592

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 593 EAKALRKLR 601


>gi|32491217|ref|NP_871471.1| hypothetical protein WGLp468 [Wigglesworthia glossinidia endosymbiont
            of Glossina brevipalpis]
 gi|25166424|dbj|BAC24614.1| rpoD [Wigglesworthia glossinidia endosymbiont of Glossina
            brevipalpis]
          Length = 601

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 318/622 (51%), Positives = 420/622 (67%), Gaps = 44/622 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTFSE+NDFLPE+IID   IE II+    M I V +   ++
Sbjct: 3    KNQQSQLKLLVTRGKEQGYLTFSEVNDFLPENIIDSHQIEDIIQMINDMGIQVMDEAPNS 62

Query: 887  ETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            E L+L  SN  SD+DV EA    LS V+S+FG+T DP++MYMREMGSV+LLTR+GEI++A
Sbjct: 63   ENLLLPDSNNNSDEDVAEAAAQVLSNVESEFGKTTDPVRMYMREMGSVQLLTREGEIDLA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE G+  +  AI   P  I+ +L    K +  E K+ E++ G +D N           
Sbjct: 123  KRIEYGINQIQCAIVEYPKAIIYLLDQYKKTTTGESKLSELITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESSSADLSTE------------------QLEKLKYESLIKFSNISFHFDK 1046
                   I+++SS+ DL+TE                  +L   ++  L +   ISF+   
Sbjct: 172  -------IVVDSSNIDLNTEDISSEEENNTSEEIDIDKELANKRFIELQEQYKISFN--- 221

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
                 ++ G   E  IK    +++     R   K  + L   +R++I ++   E++I+ I
Sbjct: 222  ---TIKEYGRMHEFSIKEIIYLADIFKQFRLVPKQFDYLVFIIRSEIEKIRFYERRIMRI 278

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             VN C MP+  FI +F  NE N  W+     +   ++  L +    I  +  KL  ++ +
Sbjct: 279  CVNICKMPKKFFISLFSGNETNDVWLKKALSLDKPWSRKLYKLNKPICLILNKLKIIEIN 338

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              + +   +DIN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 339  SGITIEQAKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 398

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 399  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 458

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF+ED ++  
Sbjct: 459  LQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFLEDTSLDL 518

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A + S+RS   D+L+ LT RE+KVL+MRFGI+MS+DHTLEEVGKQFDVTRERIRQI
Sbjct: 519  PLDSATSESLRSATHDVLSGLTAREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQI 578

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 579  EAKALRKLRHPSRSEILRSFLD 600



 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/609 (51%), Positives = 411/609 (67%), Gaps = 44/609 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTFSE+NDFLPE+IID   IE II+    M I V +   ++
Sbjct: 3   KNQQSQLKLLVTRGKEQGYLTFSEVNDFLPENIIDSHQIEDIIQMINDMGIQVMDEAPNS 62

Query: 97  ETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           E L+L  SN  SD+DV EA    LS V+S+FG+T DP++MYMREMGSV+LLTR+GEI++A
Sbjct: 63  ENLLLPDSNNNSDEDVAEAAAQVLSNVESEFGKTTDPVRMYMREMGSVQLLTREGEIDLA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE G+  +  AI   P  I+ +L    K +  E K+ E++ G +D N           
Sbjct: 123 KRIEYGINQIQCAIVEYPKAIIYLLDQYKKTTTGESKLSELITGFVDPN----------- 171

Query: 215 KNNNEEKILIESSSADLSTE------------------QLEKLKYESLIKFSNISFHFDK 256
                  I+++SS+ DL+TE                  +L   ++  L +   ISF+   
Sbjct: 172 -------IVVDSSNIDLNTEDISSEEENNTSEEIDIDKELANKRFIELQEQYKISFN--- 221

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
                ++ G   E  IK    +++     R   K  + L   +R++I ++   E++I+ I
Sbjct: 222 ---TIKEYGRMHEFSIKEIIYLADIFKQFRLVPKQFDYLVFIIRSEIEKIRFYERRIMRI 278

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            VN C MP+  FI +F  NE N  W+     +   ++  L +    I  +  KL  ++ +
Sbjct: 279 CVNICKMPKKFFISLFSGNETNDVWLKKALSLDKPWSRKLYKLNKPICLILNKLKIIEIN 338

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             + +   +DIN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 339 SGITIEQAKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 398

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 399 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 458

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF+ED ++  
Sbjct: 459 LQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFLEDTSLDL 518

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A + S+RS   D+L+ LT RE+KVL+MRFGI+MS+DHTLEEVGKQFDVTRERIRQI
Sbjct: 519 PLDSATSESLRSATHDVLSGLTAREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQI 578

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 579 EAKALRKLR 587


>gi|400405594|ref|YP_006588453.1| sigma-70 family RNA polymerase sigma factor [secondary endosymbiont
            of Ctenarytaina eucalypti]
 gi|400363957|gb|AFP85025.1| RNA polymerase sigma factor, sigma-70 family [secondary endosymbiont
            of Ctenarytaina eucalypti]
          Length = 613

 Score =  588 bits (1517), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/614 (50%), Positives = 418/614 (68%), Gaps = 16/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTFSE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNSQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L+  TSD D E+A EAA   LS+V+++ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLLLAETTSDTD-EDAVEAAAQVLSSVEAEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE+G+  +  +++  P  I  +L   +++   E+++ +++ G ID N   +   +  
Sbjct: 122  AKRIEDGINQVQCSVAEYPEAITYLLEQYERVEAQEVRMSDLITGFIDPNAEED---MTA 178

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAFEKE 1054
               +   ++ ++ S+AD   E       E         +  KF  +   ++  R   +  
Sbjct: 179  TVTHIGSELAVDDSTADDDEEDSSGDSAEDDHSIDPELARQKFLELREQYEITRNMIKAN 238

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G N  +      N+S+     R   K  + L + +R  +++V   E+ I+++ V    MP
Sbjct: 239  GLNHITSASEILNLSDVFKQFRLVPKQFDYLVNNMRAMMDRVRNQERFIMKLCVEISKMP 298

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F+ +F  NE + +W      +   ++  L      +    +KL  ++ +  L +  +
Sbjct: 299  KKSFVTLFSGNETSDSWFKAALSMNKAWSERLHAVDDEVHRSLKKLRQIEEETGLTIEQV 358

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 359  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 419  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREP 478

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P+ +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 479  TPAELADRMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 538

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 539  SLRSATHEVLAGLTVREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 599  RHPSRSEVLRSFLD 612



 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/601 (50%), Positives = 409/601 (68%), Gaps = 16/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTFSE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNSQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L+  TSD D E+A EAA   LS+V+++ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLLLAETTSDTD-EDAVEAAAQVLSSVEAEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE+G+  +  +++  P  I  +L   +++   E+++ +++ G ID N   +   +  
Sbjct: 122 AKRIEDGINQVQCSVAEYPEAITYLLEQYERVEAQEVRMSDLITGFIDPNAEED---MTA 178

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAFEKE 264
              +   ++ ++ S+AD   E       E         +  KF  +   ++  R   +  
Sbjct: 179 TVTHIGSELAVDDSTADDDEEDSSGDSAEDDHSIDPELARQKFLELREQYEITRNMIKAN 238

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G N  +      N+S+     R   K  + L + +R  +++V   E+ I+++ V    MP
Sbjct: 239 GLNHITSASEILNLSDVFKQFRLVPKQFDYLVNNMRAMMDRVRNQERFIMKLCVEISKMP 298

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F+ +F  NE + +W      +   ++  L      +    +KL  ++ +  L +  +
Sbjct: 299 KKSFVTLFSGNETSDSWFKAALSMNKAWSERLHAVDDEVHRSLKKLRQIEEETGLTIEQV 358

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREP 478

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P+ +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 479 TPAELADRMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 538

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 539 SLRSATHEVLAGLTVREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598

Query: 625 R 625
           R
Sbjct: 599 R 599


>gi|374261642|ref|ZP_09620220.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii LLAP12]
 gi|363537736|gb|EHL31152.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii LLAP12]
          Length = 621

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 313/606 (51%), Positives = 416/606 (68%), Gaps = 15/606 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 16   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK-NNNEEKIL 1013
            + +++  P T+  +L   ++    EI+++EI+ G  D +         G+  + +++  L
Sbjct: 134  LKSLAHYPETVQLVLDDYERFIAQEIRLNEIISGFADSDEEMAPAANIGSMLDESQQDEL 193

Query: 1014 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF-------EKEGYNSESYIKAHN 1066
            I ++  +    +    + +          +FD++R+ F       ++ G       K+  
Sbjct: 194  ILANDDEDEDGEGGIAEVDDGPNPEQAKAYFDELRECFNAAMVVLKEHGRTHAKTNKSLE 253

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +S+  L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254  AMSDSFLKLKLTSRQVDRLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 1127 INLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             +L W++N    +H   L + R       I  +Q +L++ + +  L + +++DINRKM  
Sbjct: 314  TDLEWLNN-IIAKHAKKLDMSRISEYTEEILRIQSRLVSFEVEYGLTIGEIKDINRKMSI 372

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 373  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 432

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A KM
Sbjct: 433  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKM 492

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            E+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +I
Sbjct: 493  ELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEI 552

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KL
Sbjct: 553  LETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKL 612

Query: 1424 KIFLEG 1429
            + FLEG
Sbjct: 613  RSFLEG 618



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 303/592 (51%), Positives = 405/592 (68%), Gaps = 15/592 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 16  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 75  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK-NNNEEKIL 223
           + +++  P T+  +L   ++    EI+++EI+ G  D +         G+  + +++  L
Sbjct: 134 LKSLAHYPETVQLVLDDYERFIAQEIRLNEIISGFADSDEEMAPAANIGSMLDESQQDEL 193

Query: 224 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF-------EKEGYNSESYIKAHN 276
           I ++  +    +    + +          +FD++R+ F       ++ G       K+  
Sbjct: 194 ILANDDEDEDGEGGIAEVDDGPNPEQAKAYFDELRECFNAAMVVLKEHGRTHAKTNKSLE 253

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +S+  L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 254 AMSDSFLKLKLTSRQVDRLTRHFRQLRNHIREFERSIMRLCIEKARIPRKLFIDTFPGQE 313

Query: 337 INLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            +L W++N    +H   L + R       I  +Q +L++ + +  L + +++DINRKM  
Sbjct: 314 TDLEWLNN-IIAKHAKKLDMSRISEYTEEILRIQSRLVSFEVEYGLTIGEIKDINRKMSI 372

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 373 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 432

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A KM
Sbjct: 433 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKM 492

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           E+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +I
Sbjct: 493 ELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEI 552

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 553 LETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|397171143|ref|ZP_10494553.1| RNA polymerase sigma factor RpoD [Alishewanella aestuarii B11]
 gi|396087617|gb|EJI85217.1| RNA polymerase sigma factor RpoD [Alishewanella aestuarii B11]
          Length = 616

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 310/608 (50%), Positives = 411/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   DT+ L++
Sbjct: 8    QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDTDDLIM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 1009
              +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128  NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 1010 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 1060
            E     S + D S E  +    +            KF+ +   ++  R +  + G    +
Sbjct: 188  EHQDDSSDTDDDSDEDGDADSDDGDSGPDPELAKQKFAELRTQYEVTRNSIVQNGREHPT 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                   +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248  TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308  AFTGHETSTAWVDAEISGNKPYSAKLAEAKDELIRCIEKLKKVEEETGLSIFKIKDINRR 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 608  EVLKSFLD 615



 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 402/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   DT+ L++
Sbjct: 8   QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDTDDLIM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 219
             +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128 NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 220 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 270
           E     S + D S E  +    +            KF+ +   ++  R +  + G    +
Sbjct: 188 EHQDDSSDTDDDSDEDGDADSDDGDSGPDPELAKQKFAELRTQYEVTRNSIVQNGREHPT 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                  +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248 TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308 AFTGHETSTAWVDAEISGNKPYSAKLAEAKDELIRCIEKLKKVEEETGLSIFKIKDINRR 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|407694800|ref|YP_006819588.1| RNA polymerase sigma factor [Alcanivorax dieselolei B5]
 gi|407252138|gb|AFT69245.1| RNA polymerase sigma factor [Alcanivorax dieselolei B5]
          Length = 630

 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 304/613 (49%), Positives = 418/613 (68%), Gaps = 20/613 (3%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI-- 894
            I LGKE+GYLT++E+ND LPE I D + +E II+    M I+V E   D + +M+     
Sbjct: 16   IALGKEQGYLTYAEVNDHLPESITDTDQVEDIIQMINDMGITVVEKATDADEIMMGEGAD 75

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            ++D+   E   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76   STDEVAAEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNE 1009
            +HA++  P  +  +L   D+I   E K+ +++ G +D +      ++ N+  + N+    
Sbjct: 136  MHALAFWPGAVEMVLDEYDRILSEERKLTDVIAGYLDPDDDGAAATNANKEPRFNQKKQA 195

Query: 1010 EKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGYNS 1058
            E    +    D   ++ +                   +F  +    +K  +A ++ G + 
Sbjct: 196  EAAEKDKDKDDDDDDKSDSDDDSEEDEGGLDPVLAAERFGELKKLHEKAERALKRNGRDH 255

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S  KA   ++      +   +  ++L    R  ++ V + E+QI+ + + + G+PR  F
Sbjct: 256  ASSAKALEALAGHFTLFKLVPRIYDQLLQGARTHLDIVRKFERQIMALAIRRAGVPRKDF 315

Query: 1119 IKVFPENEINLNWV--DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            ++ FP NE NL WV    +TK   DY+  L      I+  Q+K+I ++  I LP+ D+++
Sbjct: 316  VQQFPGNETNLEWVAAHAKTKRAKDYSERLLAVAEDIQRNQRKIITVEEVIGLPVADIKE 375

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 376  INRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 435

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ+LQE G EP P
Sbjct: 436  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTP 495

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  ++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED N+ +P D+A +  +
Sbjct: 496  EELGQRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNVDSPVDSATSLGL 555

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
                +++L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 556  EEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 615

Query: 1417 PSRYYKLKIFLEG 1429
            PSR   L+ FL+ 
Sbjct: 616  PSRSEHLRSFLDA 628



 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 409/599 (68%), Gaps = 20/599 (3%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNI-- 104
           I LGKE+GYLT++E+ND LPE I D + +E II+    M I+V E   D + +M+     
Sbjct: 16  IALGKEQGYLTYAEVNDHLPESITDTDQVEDIIQMINDMGITVVEKATDADEIMMGEGAD 75

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           ++D+   E   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76  STDEVAAEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGNKNNNE 219
           +HA++  P  +  +L   D+I   E K+ +++ G +D +      ++ N+  + N+    
Sbjct: 136 MHALAFWPGAVEMVLDEYDRILSEERKLTDVIAGYLDPDDDGAAATNANKEPRFNQKKQA 195

Query: 220 EKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGYNS 268
           E    +    D   ++ +                   +F  +    +K  +A ++ G + 
Sbjct: 196 EAAEKDKDKDDDDDDKSDSDDDSEEDEGGLDPVLAAERFGELKKLHEKAERALKRNGRDH 255

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S  KA   ++      +   +  ++L    R  ++ V + E+QI+ + + + G+PR  F
Sbjct: 256 ASSAKALEALAGHFTLFKLVPRIYDQLLQGARTHLDIVRKFERQIMALAIRRAGVPRKDF 315

Query: 329 IKVFPENEINLNWV--DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           ++ FP NE NL WV    +TK   DY+  L      I+  Q+K+I ++  I LP+ D+++
Sbjct: 316 VQQFPGNETNLEWVAAHAKTKRAKDYSERLLAVAEDIQRNQRKIITVEEVIGLPVADIKE 375

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 376 INRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 435

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ+LQE G EP P
Sbjct: 436 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTP 495

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  ++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED N+ +P D+A +  +
Sbjct: 496 EELGQRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNVDSPVDSATSLGL 555

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               +++L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 556 EEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 614


>gi|408373888|ref|ZP_11171580.1| RNA polymerase sigma factor RpoD [Alcanivorax hongdengensis A-11-3]
 gi|407766176|gb|EKF74621.1| RNA polymerase sigma factor RpoD [Alcanivorax hongdengensis A-11-3]
          Length = 632

 Score =  587 bits (1514), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/622 (49%), Positives = 419/622 (67%), Gaps = 36/622 (5%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 894
            I LGKE+GYLT++E+ND LPE I D + +E II+    M I+V E   D + +M+  S  
Sbjct: 16   IALGKEQGYLTYAEVNDHLPESITDTDQVEDIIQMINDMGITVVEKATDADQIMIDESAD 75

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            ++D+   E   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76   STDEVAAEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            +HA++  P  +  +L    ++   E K+ +I+ G +D N            N N+E    
Sbjct: 136  LHALAFWPGAVDMLLDEYARVEAEERKLTDIIAGYLDPNDDG-----AAATNANKEPTFA 190

Query: 1015 ESSSADLSTEQLEKLKYESLI-----------------------KFSNISFHFDKMRKAF 1051
            E +      ++ E    E                          +F+ +    +K  +A 
Sbjct: 191  EKAKKAAEAKEKEDDDDEDDADNKDDDDDSDEDEGGLDPVLAAERFNQLKKLHEKAERAL 250

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            ++ G +  S  KA   ++      +   +  +++    RN ++ V + E+QI+   + + 
Sbjct: 251  KRNGRDHASTAKAQEALAEHFTLFKLVPRIYDEMLVGARNNLDMVRKFERQIMSAAIRRG 310

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDI 1167
            GM R  FIK FP NE ++ WVD  T+++      +   + ++KE     Q+K++ ++  I
Sbjct: 311  GMDRKDFIKAFPGNETDMGWVD--TQLKTKKGKAIADRLGAVKEDVQRAQRKIVTIEEII 368

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 369  GLPVADIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 428

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ+L
Sbjct: 429  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQML 488

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM +P
Sbjct: 489  QEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNMESP 548

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A +  +    +++L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 549  VDSATSLGLEEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 608

Query: 1408 AKALRKLRHPSRYYKLKIFLEG 1429
            AKALRKLRHPSR   L+ FL+G
Sbjct: 609  AKALRKLRHPSRSEHLRSFLDG 630



 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/608 (49%), Positives = 409/608 (67%), Gaps = 36/608 (5%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 104
           I LGKE+GYLT++E+ND LPE I D + +E II+    M I+V E   D + +M+  S  
Sbjct: 16  IALGKEQGYLTYAEVNDHLPESITDTDQVEDIIQMINDMGITVVEKATDADQIMIDESAD 75

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           ++D+   E   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76  STDEVAAEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           +HA++  P  +  +L    ++   E K+ +I+ G +D N            N N+E    
Sbjct: 136 LHALAFWPGAVDMLLDEYARVEAEERKLTDIIAGYLDPNDDG-----AAATNANKEPTFA 190

Query: 225 ESSSADLSTEQLEKLKYESLI-----------------------KFSNISFHFDKMRKAF 261
           E +      ++ E    E                          +F+ +    +K  +A 
Sbjct: 191 EKAKKAAEAKEKEDDDDEDDADNKDDDDDSDEDEGGLDPVLAAERFNQLKKLHEKAERAL 250

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           ++ G +  S  KA   ++      +   +  +++    RN ++ V + E+QI+   + + 
Sbjct: 251 KRNGRDHASTAKAQEALAEHFTLFKLVPRIYDEMLVGARNNLDMVRKFERQIMSAAIRRG 310

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDI 377
           GM R  FIK FP NE ++ WVD  T+++      +   + ++KE     Q+K++ ++  I
Sbjct: 311 GMDRKDFIKAFPGNETDMGWVD--TQLKTKKGKAIADRLGAVKEDVQRAQRKIVTIEEII 368

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 369 GLPVADIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 428

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ+L
Sbjct: 429 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQML 488

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM +P
Sbjct: 489 QEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNMESP 548

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A +  +    +++L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 549 VDSATSLGLEEATREVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 608

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 609 AKALRKLR 616


>gi|393764014|ref|ZP_10352626.1| RNA polymerase sigma factor RpoD [Alishewanella agri BL06]
 gi|392604644|gb|EIW87543.1| RNA polymerase sigma factor RpoD [Alishewanella agri BL06]
          Length = 616

 Score =  587 bits (1514), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/608 (50%), Positives = 410/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D + L++
Sbjct: 8    QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDADDLIM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 1009
              +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128  NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 1010 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 1060
            E     S S D S E  +    +            KF+ +   ++  R +  + G    +
Sbjct: 188  EHQDDSSDSDDDSDEDGDSDSDDGDSGPDPELAKQKFAELRAQYEVTRNSIVQNGREHAT 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                   +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248  TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308  AFTGHETSTAWVDAEISGSKPYSAKLAEAKDELFRCIEKLKKVEEETGLSIFKIKDINRR 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 608  EVLKSFLD 615



 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 401/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D + L++
Sbjct: 8   QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDADDLIM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 219
             +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128 NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 220 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 270
           E     S S D S E  +    +            KF+ +   ++  R +  + G    +
Sbjct: 188 EHQDDSSDSDDDSDEDGDSDSDDGDSGPDPELAKQKFAELRAQYEVTRNSIVQNGREHAT 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                  +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248 TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308 AFTGHETSTAWVDAEISGSKPYSAKLAEAKDELFRCIEKLKKVEEETGLSIFKIKDINRR 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|375110652|ref|ZP_09756872.1| RNA polymerase sigma factor RpoD [Alishewanella jeotgali KCTC 22429]
 gi|374569226|gb|EHR40389.1| RNA polymerase sigma factor RpoD [Alishewanella jeotgali KCTC 22429]
          Length = 616

 Score =  587 bits (1514), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 410/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D + L++
Sbjct: 8    QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDADDLIM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 1009
              +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128  NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 1010 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 1060
            E       S D S E+ +    +            KF+ +   ++  R +  + G    +
Sbjct: 188  EHQEDADISDDDSDEESDGDSDDGDSGPDPELAKQKFAELRAQYEVTRNSIVQNGREHAT 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                   +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248  TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308  AFTGHETSTAWVDAEISGNKPYSAKLAEAKDELIRCIEKLKKIEEETGLSIFKIKDINRR 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 608  EVLKSFLD 615



 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 401/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D + L++
Sbjct: 8   QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDADDLIM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  SDATADEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN--E 219
             +  +++  P  I  +L   DK    EI++ +IV   +D N   +  V+  N  ++  E
Sbjct: 128 NQVQTSVAEYPEAITYLLEQWDKYEAEEIRLSDIVSAFVDPNEVDDAPVMGSNIGSDLPE 187

Query: 220 EKILIESSSADLSTEQLEKLKYESLI---------KFSNISFHFDKMRKAFEKEGYNSES 270
           E       S D S E+ +    +            KF+ +   ++  R +  + G    +
Sbjct: 188 EHQEDADISDDDSDEESDGDSDDGDSGPDPELAKQKFAELRAQYEVTRNSIVQNGREHAT 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                  +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ +F+K
Sbjct: 248 TKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERLVMKHAVEYAKMPKKNFVK 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  +E +  WVD E      Y+  L      +    +KL  ++ +  L +  ++DINR+
Sbjct: 308 AFTGHETSTAWVDAEISGNKPYSAKLAEAKDELIRCIEKLKKIEEETGLSIFKIKDINRR 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELS 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  +P D+A   S+++  
Sbjct: 488 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGESPLDSATMESLKNAT 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 NEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|448824732|dbj|BAM78695.1| RNA polymerase sigma factor, partial [Pseudomonas syringae pv.
           maculicola]
          Length = 587

 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 411/592 (69%), Gaps = 19/592 (3%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS 106
           I LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +
Sbjct: 1   ITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADT 60

Query: 107 DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIH 166
           D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ 
Sbjct: 61  DEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMG 120

Query: 167 AISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVIKGNKN 216
           AI+  P T+  IL    +++    ++ +++ G ID +             + + +K    
Sbjct: 121 AIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAVKAEGA 180

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYNSESYI 272
           +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G + +  I
Sbjct: 181 DDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 235

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ F
Sbjct: 236 AELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQF 295

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M 
Sbjct: 296 PGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMS 355

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 356 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 415

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 416 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 475

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 476 MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 535

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 536 VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 587



 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/592 (51%), Positives = 411/592 (69%), Gaps = 19/592 (3%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS 896
            I LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +
Sbjct: 1    ITLGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADT 60

Query: 897  DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIH 956
            D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ 
Sbjct: 61   DEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMG 120

Query: 957  AISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVIKGNKN 1006
            AI+  P T+  IL    +++    ++ +++ G ID +             + + +K    
Sbjct: 121  AIAHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAVKAEGA 180

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +++E+      SAD S E+ E       +    +F  +S   +  RKA +K G + +  I
Sbjct: 181  DDDEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAI 235

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ F
Sbjct: 236  AELVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQF 295

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M 
Sbjct: 296  PGHEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMS 355

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 356  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 415

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 416  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 475

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   ++
Sbjct: 476  MEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATRE 535

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 536  VLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 587


>gi|304415465|ref|ZP_07396113.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
            insecticola LSR1]
 gi|304282694|gb|EFL91209.1| RNA polymerase sigma 70 (sigma D) subunit [Candidatus Regiella
            insecticola LSR1]
          Length = 612

 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 312/618 (50%), Positives = 417/618 (67%), Gaps = 25/618 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-- 1002
            KRIEEG+  +  +++  P  I  +L   D++   E+++ +++ G +D N   N   I   
Sbjct: 123  KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAEEVRLSDLITGFVDLNAKENEEDITLS 182

Query: 1003 ------GNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEK 1053
                  G++ + EE I  +  +AD   E    +  + L+   KFS +   ++  +KA +K
Sbjct: 183  ASATHIGSELSTEELIDSDGDTADSDDENNNSI--DPLLAREKFSELREQYENTKKAIKK 240

Query: 1054 EGYNSESYIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            +G N    + A N I   SN     R   K  + L + +R  + Q+   E+ I+++ V +
Sbjct: 241  DGRNR---LNAKNEILALSNIFKLFRLVPKQFDYLVNNMRLMMKQIRAQERIIIKLCVEQ 297

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            C MP+  F+ +F  +E +  W +        ++  L      +   ++KLI ++    L 
Sbjct: 298  CKMPKKIFLTLFTRHETDDKWFEEALSANKPWSEKLKEVAEDVGCCRKKLIQIEEKTGLT 357

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358  VEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE 
Sbjct: 418  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEX 477

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
                          MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P  +
Sbjct: 478  XX----XXXXXXXXMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLGS 533

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 534  ATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 593

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FL+
Sbjct: 594  LRKLRHPSRSEVLRSFLD 611



 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/605 (50%), Positives = 408/605 (67%), Gaps = 25/605 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D  DD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK-- 212
           KRIEEG+  +  +++  P  I  +L   D++   E+++ +++ G +D N   N   I   
Sbjct: 123 KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAEEVRLSDLITGFVDLNAKENEEDITLS 182

Query: 213 ------GNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEK 263
                 G++ + EE I  +  +AD   E    +  + L+   KFS +   ++  +KA +K
Sbjct: 183 ASATHIGSELSTEELIDSDGDTADSDDENNNSI--DPLLAREKFSELREQYENTKKAIKK 240

Query: 264 EGYNSESYIKAHNNI---SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           +G N    + A N I   SN     R   K  + L + +R  + Q+   E+ I+++ V +
Sbjct: 241 DGRNR---LNAKNEILALSNIFKLFRLVPKQFDYLVNNMRLMMKQIRAQERIIIKLCVEQ 297

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
           C MP+  F+ +F  +E +  W +        ++  L      +   ++KLI ++    L 
Sbjct: 298 CKMPKKIFLTLFTRHETDDKWFEEALSANKPWSEKLKEVAEDVGCCRKKLIQIEEKTGLT 357

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 358 VEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE 
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEX 477

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
                         MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P  +
Sbjct: 478 XX----XXXXXXXXMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLGS 533

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 534 ATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 593

Query: 621 LRKLR 625
           LRKLR
Sbjct: 594 LRKLR 598


>gi|89075585|ref|ZP_01161990.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048725|gb|EAR54297.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 616

 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 311/617 (50%), Positives = 415/617 (67%), Gaps = 19/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N  +       +  
Sbjct: 123  IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---------------KFSNISFHFDKMRKAF 1051
            +     L ES   D   +  +    E                  KF  +   +DKM  A 
Sbjct: 183  SE----LSESDLEDEDKDLEDDENSEDSDEEEDDGSIDPELAREKFLELRNAYDKMALAI 238

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            +  G  + +   A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+  
Sbjct: 239  DTNGRQNATTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 298

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  F+ +F  NE   +W+D        Y   L      ++    KL  L+ +  L +
Sbjct: 299  KMPKKTFVSLFAGNESKQDWIDEALNSGKPYAERLKVYEEDLRRASIKLRMLEEETGLSI 358

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359  ERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA
Sbjct: 479  REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAA 538

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               ++R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539  TATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 599  RKLRHPSRSDVLRSFLD 615



 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 304/604 (50%), Positives = 406/604 (67%), Gaps = 19/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N  +       +  
Sbjct: 123 IEDGINQVQCSVAEYPSAIAHLLEQFDKVEADELRLTDIISGFVDPNEEATAAPTATHIG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---------------KFSNISFHFDKMRKAF 261
           +     L ES   D   +  +    E                  KF  +   +DKM  A 
Sbjct: 183 SE----LSESDLEDEDKDLEDDENSEDSDEEEDDGSIDPELAREKFLELRNAYDKMALAI 238

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           +  G  + +   A   +S      R   K  ++L  +LR+ +++V   E+ I+ + V+  
Sbjct: 239 DTNGRQNATTEIAVEELSEVFKQFRLIPKQFDRLVSSLRDSMDKVRTNERLIMRMCVDNS 298

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  F+ +F  NE   +W+D        Y   L      ++    KL  L+ +  L +
Sbjct: 299 KMPKKTFVSLFAGNESKQDWIDEALNSGKPYAERLKVYEEDLRRASIKLRMLEEETGLSI 358

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359 ERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA
Sbjct: 479 REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAA 538

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              ++R+   D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539 TATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 622 RKLR 625
           RKLR
Sbjct: 599 RKLR 602


>gi|389805596|ref|ZP_10202744.1| RNA polymerase sigma factor RpoD [Rhodanobacter thiooxydans LCS2]
 gi|388447291|gb|EIM03301.1| RNA polymerase sigma factor RpoD [Rhodanobacter thiooxydans LCS2]
          Length = 624

 Score =  587 bits (1513), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 315/615 (51%), Positives = 412/615 (66%), Gaps = 22/615 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+ L  
Sbjct: 12   EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDPLAD 71

Query: 892  SNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
               +S DD   A EA   LS VDS+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 72   KAGSSTDDEAAAEEAVALLSAVDSEVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 131

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            GL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       K    
Sbjct: 132  GLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAAD----LARKEKEA 187

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISF---------------HFDKMRKAFEKE 1054
              +L          ++ E        + +  S                ++ K +KA  K 
Sbjct: 188  AALLAPEVEDSEEGDEDEDETATEDEEEAGPSGPDPEEVKRRMELLREYYAKFQKAAPKA 247

Query: 1055 G-YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
                 +  +K  + ++ E L ++  +  I+     LR  +N +   E+ +++I V +  M
Sbjct: 248  ASITDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVNDIRHHERVLMDIFVKQVKM 307

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FIK FP NE N  WV   ++ +  ++  +  +  +I   Q+KL  ++  + LPL D
Sbjct: 308  PKAEFIKAFPSNEGNPEWVAELSRKRQKWSPNIKTHREAIDAEQEKLAAIERKLFLPLID 367

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 368  IKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 427

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E
Sbjct: 428  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGRE 487

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
              P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D+A  
Sbjct: 488  ATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPIDSATE 547

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 548  TGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 607

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR  +L+ FL+
Sbjct: 608  LRHPSRSEQLRSFLD 622



 Score =  571 bits (1472), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 308/602 (51%), Positives = 402/602 (66%), Gaps = 22/602 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++EIND LP+DI+D E IE I+   + + I V +   DT+ L  
Sbjct: 12  EIKALISKGLEQGYLTYAEINDHLPDDIVDPEQIEDIMAVLKGVGIEVHDAAPDTDPLAD 71

Query: 102 SNITSDDDVEEATEAA--LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
              +S DD   A EA   LS VDS+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 72  KAGSSTDDEAAAEEAVALLSAVDSEVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 131

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           GL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++       K    
Sbjct: 132 GLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAAD----LARKEKEA 187

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISF---------------HFDKMRKAFEKE 264
             +L          ++ E        + +  S                ++ K +KA  K 
Sbjct: 188 AALLAPEVEDSEEGDEDEDETATEDEEEAGPSGPDPEEVKRRMELLREYYAKFQKAAPKA 247

Query: 265 G-YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
                +  +K  + ++ E L ++  +  I+     LR  +N +   E+ +++I V +  M
Sbjct: 248 ASITDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVNDIRHHERVLMDIFVKQVKM 307

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FIK FP NE N  WV   ++ +  ++  +  +  +I   Q+KL  ++  + LPL D
Sbjct: 308 PKAEFIKAFPSNEGNPEWVAELSRKRQKWSPNIKTHREAIDAEQEKLAAIERKLFLPLID 367

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DINR M +GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 368 IKDINRAMASGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 427

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E
Sbjct: 428 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGRE 487

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
             P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D+A  
Sbjct: 488 ATPEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPIDSATE 547

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 548 TGLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 607

Query: 624 LR 625
           LR
Sbjct: 608 LR 609


>gi|238760057|ref|ZP_04621208.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
 gi|238701744|gb|EEP94310.1| RNA polymerase sigma factor rpoD [Yersinia aldovae ATCC 35236]
          Length = 611

 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 312/608 (51%), Positives = 418/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N   +       
Sbjct: 123  KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ + EE    +    +   E    +  E +  KFS +   ++  R A +K G +  S
Sbjct: 183  VGSELSTEEMDEDDKEEDEEEEEDDNSIDPELARQKFSELRDQYENTRMAIKKNGRSHAS 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                  N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243  AAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/595 (51%), Positives = 409/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N   +       
Sbjct: 123 KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ + EE    +    +   E    +  E +  KFS +   ++  R A +K G +  S
Sbjct: 183 VGSELSTEEMDEDDKEEDEEEEEDDNSIDPELARQKFSELRDQYENTRMAIKKNGRSHAS 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                 N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243 AAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|343494355|ref|ZP_08732617.1| RNA polymerase sigma factor RpoD [Vibrio nigripulchritudo ATCC 27043]
 gi|342825260|gb|EGU59759.1| RNA polymerase sigma factor RpoD [Vibrio nigripulchritudo ATCC 27043]
          Length = 613

 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 311/610 (50%), Positives = 420/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LP++I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPQEIVDSEQVEDIIQMINDMGIQVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA  AALSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMMNEAVADEDAAEAAAAALSTVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P TI  IL   DK+   E+++ +I+ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPGTISYILEQFDKVQAEELRLTDIISGFVDPNDEETAAPTATHIG 182

Query: 1007 NN-EEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNS 1058
            +   E+ L +    D  ++  +  + ++ I       KF+ +   +  ++ A  ++G  +
Sbjct: 183  SELAEQDLDDEDDDDSDSDDDDDEEEDTGIDPELAAEKFNELRTAYQNLQLAINEKGRET 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                ++   + +     R   K  + L + LR  +++V   E+ I+   V    MP+  F
Sbjct: 243  ALASESATELLDVFRQFRLIPKQFDYLVNELRTSMDRVRTQERLIMRSCVEYGDMPKKSF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE +  W+D        Y   + RN   I+    KL  ++ +  LP+  ++DI+
Sbjct: 303  VALFTGNESSEAWLDEVLASGKPYADKIKRNEEEIRRSILKLKTIEEETSLPVQSIKDIS 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R 
Sbjct: 483  LAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSTSLRV 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSETLRSFLD 612



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 304/597 (50%), Positives = 411/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LP++I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPQEIVDSEQVEDIIQMINDMGIQVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA  AALSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMMNEAVADEDAAEAAAAALSTVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P TI  IL   DK+   E+++ +I+ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPGTISYILEQFDKVQAEELRLTDIISGFVDPNDEETAAPTATHIG 182

Query: 217 NN-EEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNS 268
           +   E+ L +    D  ++  +  + ++ I       KF+ +   +  ++ A  ++G  +
Sbjct: 183 SELAEQDLDDEDDDDSDSDDDDDEEEDTGIDPELAAEKFNELRTAYQNLQLAINEKGRET 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
               ++   + +     R   K  + L + LR  +++V   E+ I+   V    MP+  F
Sbjct: 243 ALASESATELLDVFRQFRLIPKQFDYLVNELRTSMDRVRTQERLIMRSCVEYGDMPKKSF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE +  W+D        Y   + RN   I+    KL  ++ +  LP+  ++DI+
Sbjct: 303 VALFTGNESSEAWLDEVLASGKPYADKIKRNEEEIRRSILKLKTIEEETSLPVQSIKDIS 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R 
Sbjct: 483 LAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSTSLRV 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|209696105|ref|YP_002264035.1| RNA polymerase sigma factor RpoD [Aliivibrio salmonicida LFI1238]
 gi|208010058|emb|CAQ80381.1| RNA polymerase sigma factor RpoD (sigma-70) [Aliivibrio salmonicida
            LFI1238]
          Length = 610

 Score =  587 bits (1512), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 317/628 (50%), Positives = 424/628 (67%), Gaps = 47/628 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63   DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N       
Sbjct: 119  IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQAEEIRLTDIISGFVDPNDD----- 173

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE----------SLIKFSNISFHFDKMRKA 1050
              G+       I  E S +DL+ E  E    E          +L KF+ +   +  M+ A
Sbjct: 174  --GSAAPTATHIGSELSESDLADEDKEAKDDEEEDVGIDPELALEKFTQLRTSYHNMQLA 231

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            FE+ G ++    +A   +++     +   K  + L   +R  +++V   E+ I+ + V  
Sbjct: 232  FEEHGRDNGKAREAIGELTDVFREFKLIPKQFDFLVREMRGSMDRVRTQERLIMRMCVEY 291

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKL 1160
              MP+  FI +F  NE +  W          +N IL  + P ++ L+          +K+
Sbjct: 292  GKMPKKSFIALFSGNEASDEW----------FNEILASDKPYVERLKRYEEDIRRSIKKI 341

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
             ++  +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 342  NSIVKETGLPVVNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 401

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 402  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 461

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIE
Sbjct: 462  RISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIE 521

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D  +  P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 522  DNTLELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 581

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  ERIRQIEAKALRKLRHPSRSEVLRSFLD 609



 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/615 (50%), Positives = 415/615 (67%), Gaps = 47/615 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63  DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N       
Sbjct: 119 IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQAEEIRLTDIISGFVDPNDD----- 173

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE----------SLIKFSNISFHFDKMRKA 260
             G+       I  E S +DL+ E  E    E          +L KF+ +   +  M+ A
Sbjct: 174 --GSAAPTATHIGSELSESDLADEDKEAKDDEEEDVGIDPELALEKFTQLRTSYHNMQLA 231

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           FE+ G ++    +A   +++     +   K  + L   +R  +++V   E+ I+ + V  
Sbjct: 232 FEEHGRDNGKAREAIGELTDVFREFKLIPKQFDFLVREMRGSMDRVRTQERLIMRMCVEY 291

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKL 370
             MP+  FI +F  NE +  W          +N IL  + P ++ L+          +K+
Sbjct: 292 GKMPKKSFIALFSGNEASDEW----------FNEILASDKPYVERLKRYEEDIRRSIKKI 341

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
            ++  +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 342 NSIVKETGLPVVNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 401

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 402 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 461

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIE
Sbjct: 462 RISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIE 521

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D  +  P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 522 DNTLELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 581

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 582 ERIRQIEAKALRKLR 596


>gi|221134905|ref|ZP_03561208.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. HTCC2999]
          Length = 607

 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 312/612 (50%), Positives = 423/612 (69%), Gaps = 15/612 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D
Sbjct: 1    MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L+++  T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61   SDELLMAETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-------- 997
            RIE+G+  +  +++  P  I  +L   D     EI++ +I+ G +D N   N        
Sbjct: 121  RIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIIIGFVDPNEDENLAPTATHI 180

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTE-QLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               +   +  +E+    E    D   + +L + K+++L K       ++K R   E +G 
Sbjct: 181  GSELSEEELEDEDDDDAEEEEVDTGVDPELAREKFDALRK------QYNKTRDVIEAKGR 234

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            ++ +  K    +S+     R   K  +++   +R  +++V   E+ I++  V +  MP+ 
Sbjct: 235  SNAAAKKQIAKLSDVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKHCVAQAKMPKK 294

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FIK F  NE + +W     K    Y L+L      I+    K+  ++ +  L + D++D
Sbjct: 295  DFIKAFAGNETSTDWYYKILKTSKPYVLVLETFQEDIERSVSKMNAVEAETGLCIADIKD 354

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 355  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 414

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 415  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 474

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+
Sbjct: 475  EELSERMIMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIIQPLDSATGGSL 534

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 535  KDATQDVLAGLTQREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 594

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 595  PSRSEQLRSFLD 606



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 305/599 (50%), Positives = 413/599 (68%), Gaps = 15/599 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L+++  T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61  SDELLMAETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-------- 207
           RIE+G+  +  +++  P  I  +L   D     EI++ +I+ G +D N   N        
Sbjct: 121 RIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIIIGFVDPNEDENLAPTATHI 180

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTE-QLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              +   +  +E+    E    D   + +L + K+++L K       ++K R   E +G 
Sbjct: 181 GSELSEEELEDEDDDDAEEEEVDTGVDPELAREKFDALRK------QYNKTRDVIEAKGR 234

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           ++ +  K    +S+     R   K  +++   +R  +++V   E+ I++  V +  MP+ 
Sbjct: 235 SNAAAKKQIAKLSDVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKHCVAQAKMPKK 294

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FIK F  NE + +W     K    Y L+L      I+    K+  ++ +  L + D++D
Sbjct: 295 DFIKAFAGNETSTDWYYKILKTSKPYVLVLETFQEDIERSVSKMNAVEAETGLCIADIKD 354

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 355 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 414

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 415 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 474

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+
Sbjct: 475 EELSERMIMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIIQPLDSATGGSL 534

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 535 KDATQDVLAGLTQREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 593


>gi|421779716|ref|ZP_16216208.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|407813426|gb|EKF84208.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
          Length = 628

 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/610 (50%), Positives = 419/610 (68%), Gaps = 15/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +   LI+LGKE+GYLT++E+ND LPE + + + IE II+    + I V E   D + ++L
Sbjct: 19   QLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDDDDILL 78

Query: 892  SNITSDDDV--EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            S+  SDDD+  +EA  A L++V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEE
Sbjct: 79   SDTGSDDDIATDEAA-AVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAKRIEE 137

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIK---G 1003
            G +++ + ++  P T+  +L    ++   E KI +IV G +   D +F  N   I+   G
Sbjct: 138  GTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIVSGFLNGDDGDFILNEEEIELDLG 197

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +    ++    E   +D  TE  +         E  ++F  I   +D  ++A  K G  S
Sbjct: 198  SPKTTDKDDAEEDGESD-GTELDDTDDSSLDPEEVRVRFEEIQRLYDVAQEALAKHGRGS 256

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            E+   A++ ++N  + I+   +  +++   +R     V   E++I+++V+    MP   F
Sbjct: 257  EAVKVAYDELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEF 316

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
             K FP NE NL W+ +  K    +   L +  P +  LQQKL+  +  + + + D++ + 
Sbjct: 317  KKTFPSNETNLEWLSHRIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVA 376

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 377  RQMAIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 436

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P  
Sbjct: 437  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEE 496

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P + A    +R 
Sbjct: 497  LGERLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLRE 556

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +++L++LT RE+KVL+MRFGI+M SDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 557  ATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 616

Query: 1419 RYYKLKIFLE 1428
            R   L+ FLE
Sbjct: 617  RSEHLRSFLE 626



 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/597 (49%), Positives = 410/597 (68%), Gaps = 15/597 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +   LI+LGKE+GYLT++E+ND LPE + + + IE II+    + I V E   D + ++L
Sbjct: 19  QLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDDDDILL 78

Query: 102 SNITSDDDV--EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           S+  SDDD+  +EA  A L++V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEE
Sbjct: 79  SDTGSDDDIATDEAA-AVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAKRIEE 137

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIK---G 213
           G +++ + ++  P T+  +L    ++   E KI +IV G +   D +F  N   I+   G
Sbjct: 138 GTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIVSGFLNGDDGDFILNEEEIELDLG 197

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNS 268
           +    ++    E   +D  TE  +         E  ++F  I   +D  ++A  K G  S
Sbjct: 198 SPKTTDKDDAEEDGESD-GTELDDTDDSSLDPEEVRVRFEEIQRLYDVAQEALAKHGRGS 256

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           E+   A++ ++N  + I+   +  +++   +R     V   E++I+++V+    MP   F
Sbjct: 257 EAVKVAYDELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEF 316

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
            K FP NE NL W+ +  K    +   L +  P +  LQQKL+  +  + + + D++ + 
Sbjct: 317 KKTFPSNETNLEWLSHRIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVA 376

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 377 RQMAIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 436

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P  
Sbjct: 437 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEE 496

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P + A    +R 
Sbjct: 497 LGERLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLRE 556

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +++L++LT RE+KVL+MRFGI+M SDHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 557 ATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|183597880|ref|ZP_02959373.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
 gi|386744243|ref|YP_006217422.1| RNA polymerase sigma factor RpoD [Providencia stuartii MRSN 2154]
 gi|188022641|gb|EDU60681.1| RNA polymerase sigma factor RpoD [Providencia stuartii ATCC 25827]
 gi|384480936|gb|AFH94731.1| RNA polymerase sigma factor RpoD [Providencia stuartii MRSN 2154]
          Length = 617

 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 413/614 (67%), Gaps = 12/614 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D +   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDHVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
              +   +  ++    +   ++                    KFS +   ++K R+  ++ 
Sbjct: 183  VGSELPQEELDKDDDEDEDDEDGDDSDSDDDNSIDPELAREKFSELRAQYEKTRQHIKQF 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G N+    +A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243  GRNNAQTAQAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            + +FI +F  NE +  W+     +   +   L      I    Q+L  ++ +  L +  +
Sbjct: 303  KKNFITLFSGNETSETWLTAAKAMNKPWCEKLVEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483  SPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATSE 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 603  RHPSRSEVLRSFLD 616



 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 404/601 (67%), Gaps = 12/601 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D +   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDHVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
             +   +  ++    +   ++                    KFS +   ++K R+  ++ 
Sbjct: 183 VGSELPQEELDKDDDEDEDDEDGDDSDSDDDNSIDPELAREKFSELRAQYEKTRQHIKQF 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G N+    +A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243 GRNNAQTAQAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           + +FI +F  NE +  W+     +   +   L      I    Q+L  ++ +  L +  +
Sbjct: 303 KKNFITLFSGNETSETWLTAAKAMNKPWCEKLVEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483 SPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLELPLDSATSE 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|262042263|ref|ZP_06015428.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            rhinoscleromatis ATCC 13884]
 gi|419972133|ref|ZP_14487562.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH1]
 gi|419978128|ref|ZP_14493425.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH2]
 gi|419984868|ref|ZP_14500012.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH4]
 gi|419989084|ref|ZP_14504061.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH5]
 gi|419995212|ref|ZP_14510019.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH6]
 gi|420001428|ref|ZP_14516084.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH7]
 gi|420007037|ref|ZP_14521532.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH8]
 gi|420012916|ref|ZP_14527228.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH9]
 gi|420018639|ref|ZP_14532835.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH10]
 gi|420026610|ref|ZP_14540611.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH11]
 gi|420029567|ref|ZP_14543396.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH12]
 gi|420038420|ref|ZP_14552067.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH14]
 gi|420041388|ref|ZP_14554885.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH16]
 gi|420047357|ref|ZP_14560674.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH17]
 gi|420052858|ref|ZP_14566038.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH18]
 gi|420061427|ref|ZP_14574416.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH19]
 gi|420064813|ref|ZP_14577621.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH20]
 gi|420074140|ref|ZP_14586755.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH21]
 gi|420077431|ref|ZP_14589896.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH22]
 gi|420082264|ref|ZP_14594563.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH23]
 gi|421910906|ref|ZP_16340677.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST258-K26BO]
 gi|421916329|ref|ZP_16345909.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST258-K28BO]
 gi|428148019|ref|ZP_18995917.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST512-K30BO]
 gi|428938666|ref|ZP_19011790.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae VA360]
 gi|259040327|gb|EEW41433.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            rhinoscleromatis ATCC 13884]
 gi|397351961|gb|EJJ45042.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH1]
 gi|397352411|gb|EJJ45490.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH2]
 gi|397353186|gb|EJJ46261.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH4]
 gi|397367965|gb|EJJ60573.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH6]
 gi|397369916|gb|EJJ62508.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH5]
 gi|397372319|gb|EJJ64815.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH7]
 gi|397380827|gb|EJJ73005.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH9]
 gi|397385149|gb|EJJ77253.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH8]
 gi|397389882|gb|EJJ81804.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH10]
 gi|397394980|gb|EJJ86695.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH11]
 gi|397402778|gb|EJJ94373.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH12]
 gi|397404337|gb|EJJ95851.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH14]
 gi|397417143|gb|EJK08312.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH17]
 gi|397418995|gb|EJK10149.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH16]
 gi|397424990|gb|EJK15878.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH18]
 gi|397430931|gb|EJK21615.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH19]
 gi|397432651|gb|EJK23308.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH20]
 gi|397436453|gb|EJK27040.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH21]
 gi|397445942|gb|EJK36171.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH22]
 gi|397452319|gb|EJK42390.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae KPNIH23]
 gi|410115281|emb|CCM83302.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST258-K26BO]
 gi|410121395|emb|CCM88534.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST258-K28BO]
 gi|426305368|gb|EKV67492.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae VA360]
 gi|427542077|emb|CCM92055.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae ST512-K30BO]
          Length = 611

 Score =  586 bits (1511), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/611 (49%), Positives = 422/611 (69%), Gaps = 12/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--------- 997
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +         
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
            + + +   +++E++      ++D       +L  E   KF+ +   ++  R   + +G +
Sbjct: 183  SELSQEEMDDDEDEDEDADDNSDDDNSIDPELARE---KFAELRTQYELTRDTIKAKGRS 239

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 240  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 299

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 300  FITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDI 359

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 420  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 479

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 480  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 539

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 540  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 599

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 600  SRSEVLRSFLD 610



 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 298/598 (49%), Positives = 413/598 (69%), Gaps = 12/598 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--------- 207
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +         
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
           + + +   +++E++      ++D       +L  E   KF+ +   ++  R   + +G +
Sbjct: 183 SELSQEEMDDDEDEDEDADDNSDDDNSIDPELARE---KFAELRTQYELTRDTIKAKGRS 239

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 240 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 299

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 300 FITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDI 359

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 360 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 419

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 420 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 479

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 480 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 539

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|82778397|ref|YP_404746.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae Sd197]
 gi|309785377|ref|ZP_07680008.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
 gi|81242545|gb|ABB63255.1| RNA polymerase, sigma(70) factor [Shigella dysenteriae Sd197]
 gi|308926497|gb|EFP71973.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 1617]
          Length = 613

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 304/610 (49%), Positives = 416/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 N--NEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
            +  ++E +  +    +   +        S+       KF+ +   +   R   + +G + 
Sbjct: 183  SELSQENLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +  T +   ++  L      +    QKL+ ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAATAMNKPWSEKLHDVSEEVHRALQKLLQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/597 (49%), Positives = 407/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 N--NEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
           +  ++E +  +    +   +        S+       KF+ +   +   R   + +G + 
Sbjct: 183 SELSQENLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +  T +   ++  L      +    QKL+ ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAATAMNKPWSEKLHDVSEEVHRALQKLLQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|448824730|dbj|BAM78694.1| RNA polymerase sigma factor, partial [Pseudomonas syringae pv.
           maculicola]
          Length = 586

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/590 (51%), Positives = 410/590 (69%), Gaps = 19/590 (3%)

Query: 49  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 108
           LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 2   LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 61

Query: 109 DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 168
              E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 62  AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 121

Query: 169 SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVIKGNKNNN 218
           +  P T+  IL    +++    ++ +++ G ID +             + + +K    ++
Sbjct: 122 AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAVKAEGADD 181

Query: 219 EEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           +E+      SAD S E+ E       +    +F  +S   +  RKA +K G + +  I  
Sbjct: 182 DEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAE 236

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
              ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ FP 
Sbjct: 237 LVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPG 296

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M  G
Sbjct: 297 HEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIG 356

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 357 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 416

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 417 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 476

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L
Sbjct: 477 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 536

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 537 SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 586



 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/590 (51%), Positives = 410/590 (69%), Gaps = 19/590 (3%)

Query: 839  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 898
            LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 2    LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 61

Query: 899  DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 958
               E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 62   AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 121

Query: 959  SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVIKGNKNNN 1008
            +  P T+  IL    +++    ++ +++ G ID +             + + +K    ++
Sbjct: 122  AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAVKAEGADD 181

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLI----KFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            +E+      SAD S E+ E       +    +F  +S   +  RKA +K G + +  I  
Sbjct: 182  DEE-----ESADSSDEEDEVESGPDPVIAQQRFGAVSDQMEITRKALKKFGRDDKHAIAE 236

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
               ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++ FP 
Sbjct: 237  LVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLRQFPG 296

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+M  G
Sbjct: 297  HEVDESWTDGLAKGKGKYAEAIGRLQPDIQRCQQKLSALEEETGLKIAEIKDINRRMSIG 356

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 357  EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 416

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 417  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 476

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   +++L
Sbjct: 477  MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEATREVL 536

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 537  SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 586


>gi|300724881|ref|YP_003714206.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus nematophila
            ATCC 19061]
 gi|297631423|emb|CBJ92120.1| sigma D (sigma 70) factor of RNA polymerase [Xenorhabdus nematophila
            ATCC 19061]
          Length = 616

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/613 (50%), Positives = 418/613 (68%), Gaps = 11/613 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSN--ISFHFDKMRKAFEKEGYNSESYI 1062
              +   K  ++    +   ++ +    E+            F ++R  +E      +SY 
Sbjct: 183  VGSELPKEELDDDDDEEDEDRDDDSDSENDNSIDPELARQKFQELRTQYEITRQAIKSYG 242

Query: 1063 KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            +++ N + E+L +       R   K  + L + +R+ +++V   E+QI+++ V +C MP+
Sbjct: 243  RSNPNTAAEILTLSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPK 302

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +FI +F  NE    W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 303  KNFITLFSGNETTDTWFTAAKAMNKPWSNKLLEIEEEVMRSLQKLRQIEEETGLTIEQVK 362

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED  +  P D+A + S
Sbjct: 483  PEELAERMMMPEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTTLELPLDSATSES 542

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543  LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 603  HPSRSEVLRSFLD 615



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/600 (50%), Positives = 409/600 (68%), Gaps = 11/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTNDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSN--ISFHFDKMRKAFEKEGYNSESYI 272
             +   K  ++    +   ++ +    E+            F ++R  +E      +SY 
Sbjct: 183 VGSELPKEELDDDDDEEDEDRDDDSDSENDNSIDPELARQKFQELRTQYEITRQAIKSYG 242

Query: 273 KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           +++ N + E+L +       R   K  + L + +R+ +++V   E+QI+++ V +C MP+
Sbjct: 243 RSNPNTAAEILTLSEVFKQFRLVPKQFDYLVNNMRSMMDRVRLQERQIMKMCVEQCKMPK 302

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +FI +F  NE    W      +   ++  L      +    QKL  ++ +  L +  ++
Sbjct: 303 KNFITLFSGNETTDTWFTAAKAMNKPWSNKLLEIEEEVMRSLQKLRQIEEETGLTIEQVK 362

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 482

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+PVGDDEDSHLGDFIED  +  P D+A + S
Sbjct: 483 PEELAERMMMPEDKIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTTLELPLDSATSES 542

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 LRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|374623714|ref|ZP_09696217.1| RNA polymerase, sigma 70 subunit, RpoD [Ectothiorhodospira sp. PHS-1]
 gi|373942818|gb|EHQ53363.1| RNA polymerase, sigma 70 subunit, RpoD [Ectothiorhodospira sp. PHS-1]
          Length = 619

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 316/617 (51%), Positives = 426/617 (69%), Gaps = 18/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            E  + + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E     
Sbjct: 4    EEQQSRLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGITVHEQAPDS 63

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D+  L  S++++DDD  E   AAL++VD +FGRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64   DSLILSDSSVSTDDDAAEEAAAALASVDGEFGRTTDPVRMYMREMGTVELLTREGEIQIA 123

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+GL  ++ A++  P +I  +L   D++   E K+ ++V   ID N      V    
Sbjct: 124  KRIEDGLSQVLFALAHYPKSIASLLAEWDQVEAGETKLTDVVVSFIDPNADEIAAVSLPK 183

Query: 1005 KNNNEEKILIESSSAD-----------LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 1053
            ++    K   +S  +D            + E       E+ I+F+++   ++K   A   
Sbjct: 184  EDTPSVKAADDSDDSDDGDDDDGDDEAAAPEDTGPDPEEARIRFTHLKAMYEK---AIAH 240

Query: 1054 EGYNS-ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
             G +  E Y +A   ++   +  +   + +++L   L   + ++   E+ I+ + V+ C 
Sbjct: 241  AGADKREEYRQAREELARYFMEFKLVPRLVDQLTADLHEMVERIRNQERAIMRLCVDTCQ 300

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
            MPR  FI+ FPENE NL W+D   K +   Y  +L  +   I   Q++L+ ++ +  L +
Sbjct: 301  MPRKDFIRTFPENETNLEWLDGCLKGKTSKYKELLAEHRDDILRAQKRLVTIEEESSLTI 360

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
             +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361  GEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             E  P  ++ +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P ++A
Sbjct: 481  REATPEELSQRMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNVQSPIESA 540

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S+    +++L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541  TRESLSETTREVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 601  RKLRHPSRSEMLRSFLD 617



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 309/604 (51%), Positives = 417/604 (69%), Gaps = 18/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           E  + + K LI  GKE+G+LT++E+ND LP+ I+D E IE II     M I+V E     
Sbjct: 4   EEQQSRLKELIAKGKEQGFLTYAEVNDHLPDTIVDPEQIEDIIAMINDMGITVHEQAPDS 63

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D+  L  S++++DDD  E   AAL++VD +FGRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64  DSLILSDSSVSTDDDAAEEAAAALASVDGEFGRTTDPVRMYMREMGTVELLTREGEIQIA 123

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+GL  ++ A++  P +I  +L   D++   E K+ ++V   ID N      V    
Sbjct: 124 KRIEDGLSQVLFALAHYPKSIASLLAEWDQVEAGETKLTDVVVSFIDPNADEIAAVSLPK 183

Query: 215 KNNNEEKILIESSSAD-----------LSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
           ++    K   +S  +D            + E       E+ I+F+++   ++K   A   
Sbjct: 184 EDTPSVKAADDSDDSDDGDDDDGDDEAAAPEDTGPDPEEARIRFTHLKAMYEK---AIAH 240

Query: 264 EGYNS-ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
            G +  E Y +A   ++   +  +   + +++L   L   + ++   E+ I+ + V+ C 
Sbjct: 241 AGADKREEYRQAREELARYFMEFKLVPRLVDQLTADLHEMVERIRNQERAIMRLCVDTCQ 300

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
           MPR  FI+ FPENE NL W+D   K +   Y  +L  +   I   Q++L+ ++ +  L +
Sbjct: 301 MPRKDFIRTFPENETNLEWLDGCLKGKTSKYKELLAEHRDDILRAQKRLVTIEEESSLTI 360

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            +++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361 GEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            E  P  ++ +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P ++A
Sbjct: 481 REATPEELSQRMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNVQSPIESA 540

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S+    +++L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541 TRESLSETTREVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 622 RKLR 625
           RKLR
Sbjct: 601 RKLR 604


>gi|119474865|ref|ZP_01615218.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451068|gb|EAW32301.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 600

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/605 (50%), Positives = 408/605 (67%), Gaps = 9/605 (1%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            E E  + + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    + I V E   
Sbjct: 3    ETEQQQSRLKTLIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDLGIQVFETAP 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDF-GRTKDPIKMYMREMGSVELLTRDGEIEI 943
            D + ++L+   S DD+  A  AA         GRT DP++MYMREMG+VELLTR+GEI I
Sbjct: 63   DADEILLTEEDSTDDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAI 122

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG++D++ A++  P  + +++   DK++  E ++ +I+ G ++          + 
Sbjct: 123  AKRIEEGIRDIMAAVAYYPGAVQDVIDDYDKVATEERRLADILVGYLNPTDVVPPAAQQA 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
                + +    E+ S     E+ +K       +F+ +    +K+ KA EK G  S+   K
Sbjct: 183  AAAVSTDDDDDETPSGP-DPEEAKK-------RFTALRKQHNKLDKAIEKHGRYSKESAK 234

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +       + T K  E L   +R+++N +   E+ I+   V +  M R  F+K F 
Sbjct: 235  ELQKLGEVFKFFKLTPKVFEPLSIRVRSKLNVIRSNERLIMNTCVRQAKMTRRDFVKSFQ 294

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
              E NL+W++ + K   D   +L  N   I   Q+K+  ++T   L + D+++INR+M  
Sbjct: 295  GQETNLDWIEQQIKAHEDVAPVLEANKEEILRAQRKIAQIETQTGLTILDIKEINRRMSI 354

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 355  GEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 414

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 415  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 474

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A    ++   KD+
Sbjct: 475  DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIAQPVDSATGQGLQEATKDV 534

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 535  LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 594

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 595  RSFLD 599



 Score =  571 bits (1472), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/600 (50%), Positives = 402/600 (67%), Gaps = 10/600 (1%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           E E  + + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    + I V E   
Sbjct: 3   ETEQQQSRLKTLIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDLGIQVFETAP 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDF-GRTKDPIKMYMREMGSVELLTRDGEIEI 153
           D + ++L+   S DD+  A  AA         GRT DP++MYMREMG+VELLTR+GEI I
Sbjct: 63  DADEILLTEEDSTDDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAI 122

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG++D++ A++  P  + +++   DK++  E ++ +I+ G ++          + 
Sbjct: 123 AKRIEEGIRDIMAAVAYYPGAVQDVIDDYDKVATEERRLADILVGYLNPTDVVPPAAQQA 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
               + +    E+ S     E+ +K       +F+ +    +K+ KA EK G  S+   K
Sbjct: 183 AAAVSTDDDDDETPSGP-DPEEAKK-------RFTALRKQHNKLDKAIEKHGRYSKESAK 234

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +       + T K  E L   +R+++N +   E+ I+   V +  M R  F+K F 
Sbjct: 235 ELQKLGEVFKFFKLTPKVFEPLSIRVRSKLNVIRSNERLIMNTCVRQAKMTRRDFVKSFQ 294

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
             E NL+W++ + K   D   +L  N   I   Q+K+  ++T   L + D+++INR+M  
Sbjct: 295 GQETNLDWIEQQIKAHEDVAPVLEANKEEILRAQRKIAQIETQTGLTILDIKEINRRMSI 354

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 355 GEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 414

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 415 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 474

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A    ++   KD+
Sbjct: 475 DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIAQPVDSATGQGLQEATKDV 534

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 535 LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 594


>gi|311278024|ref|YP_003940255.1| RNA polymerase sigma-70 subunit RpoD [Enterobacter cloacae SCF1]
 gi|308747219|gb|ADO46971.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae SCF1]
          Length = 614

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 415/611 (67%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK---G 1003
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +        G
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYN 1057
            ++ + EE    +    D  ++        S+       KF  +   ++  R   + +G +
Sbjct: 183  SELSQEEMDDDDEEDEDEDSDSDSSDDDNSIDPELAREKFGELRAQYEVTRDTIKAKGRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
              +  +    +S      R   K  + L +++R  + +V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMERVRIQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 406/598 (67%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK---G 213
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +        G
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAAEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYN 267
           ++ + EE    +    D  ++        S+       KF  +   ++  R   + +G +
Sbjct: 183 SELSQEEMDDDDEEDEDEDSDSDSSDDDNSIDPELAREKFGELRAQYEVTRDTIKAKGRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
             +  +    +S      R   K  + L +++R  + +V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRTMMERVRIQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLHDVTEDVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|387130959|ref|YP_006293849.1| RNA polymerase sigma factor RpoD [Methylophaga sp. JAM7]
 gi|386272248|gb|AFJ03162.1| RNA polymerase sigma factor RpoD [Methylophaga sp. JAM7]
          Length = 612

 Score =  586 bits (1510), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 304/614 (49%), Positives = 423/614 (68%), Gaps = 16/614 (2%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1    MKDQQSRVKELITLGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 886  TETL--MLSNITSDDDVEEATEAA-LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            T+ +  +   + S+D+V +   AA L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61   TDEMERLAEAVASNDEVSDDEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE GL++ +  +S+ P  I   L   D +   E+++++++ G     F      + 
Sbjct: 121  IAKRIEAGLRESLVMLSTYPPCIAAFLTLFDAVEAGELRLNDLIRG-----FVQPEEELA 175

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE--KEGY---- 1056
               ++ +E    ++  +D   +  + +   S     +     D+ R+ F   KE Y    
Sbjct: 176  SQDDDEDEADSNDNDDSDGDDDDDDDVSNVSDDDDDSGVIDPDEARERFTALKEAYLDVL 235

Query: 1057 --NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
                +  I A    SN  +  R T K++  L   + + I+ + + EK I++IVV    M 
Sbjct: 236  SAEDDELIAAREQASNLFMEFRLTPKTLVTLNSLMTDTIDAIRKQEKIIMDIVVEDARMN 295

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R  FI  F  NE NL W D   + +  Y+  + ++   I + Q++L ++  +  L ++++
Sbjct: 296  RRDFIDSFQGNESNLEWADKFIRAKKHYSSTIKKHHDDILDAQKQLADIAGERGLSISEI 355

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            ++I R+M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 356  KEIARQMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 415

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEY+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP
Sbjct: 416  FEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREP 475

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P+D+A+  
Sbjct: 476  TPDELAERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVMSPADSAIIE 535

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
             +R   + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 536  GLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 595

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR  +L+ FL+
Sbjct: 596  RHPSRSDQLRSFLD 609



 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/609 (49%), Positives = 416/609 (68%), Gaps = 17/609 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1   MKDQQSRVKELITLGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 96  TETL--MLSNITSDDDVEEATEAA-LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           T+ +  +   + S+D+V +   AA L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61  TDEMERLAEAVASNDEVSDDEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE GL++ +  +S+ P  I   L   D +   E+++++++ G     F      + 
Sbjct: 121 IAKRIEAGLRESLVMLSTYPPCIAAFLTLFDAVEAGELRLNDLIRG-----FVQPEEELA 175

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE--KEGY---- 266
              ++ +E    ++  +D   +  + +   S     +     D+ R+ F   KE Y    
Sbjct: 176 SQDDDEDEADSNDNDDSDGDDDDDDDVSNVSDDDDDSGVIDPDEARERFTALKEAYLDVL 235

Query: 267 --NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
               +  I A    SN  +  R T K++  L   + + I+ + + EK I++IVV    M 
Sbjct: 236 SAEDDELIAAREQASNLFMEFRLTPKTLVTLNSLMTDTIDAIRKQEKIIMDIVVEDARMN 295

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R  FI  F  NE NL W D   + +  Y+  + ++   I + Q++L ++  +  L ++++
Sbjct: 296 RRDFIDSFQGNESNLEWADKFIRAKKHYSSTIKKHHDDILDAQKQLADIAGERGLSISEI 355

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           ++I R+M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 356 KEIARQMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 415

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEY+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+LQE G EP
Sbjct: 416 FEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQMLQEMGREP 475

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A ++EMPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P+D+A+  
Sbjct: 476 TPDELAERVEMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVMSPADSAIIE 535

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
            +R   + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 536 GLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 595

Query: 625 R-PLAHDWL 632
           R P   D L
Sbjct: 596 RHPSRSDQL 604


>gi|296112900|ref|YP_003626838.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|416155718|ref|ZP_11604011.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 101P30B1]
 gi|416217278|ref|ZP_11624227.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 7169]
 gi|416222014|ref|ZP_11625978.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 103P14B1]
 gi|416227425|ref|ZP_11627183.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 46P47B1]
 gi|416239402|ref|ZP_11631952.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC1]
 gi|416241802|ref|ZP_11632936.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC7]
 gi|416247627|ref|ZP_11635810.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC8]
 gi|416250229|ref|ZP_11637238.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis CO72]
 gi|416254493|ref|ZP_11638759.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis O35E]
 gi|295920594|gb|ADG60945.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BBH18]
 gi|326561129|gb|EGE11494.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 7169]
 gi|326564438|gb|EGE14665.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 103P14B1]
 gi|326564864|gb|EGE15069.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 46P47B1]
 gi|326567590|gb|EGE17705.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC1]
 gi|326569439|gb|EGE19499.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC8]
 gi|326571363|gb|EGE21378.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis BC7]
 gi|326575352|gb|EGE25280.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis CO72]
 gi|326576561|gb|EGE26468.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 101P30B1]
 gi|326577423|gb|EGE27307.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis O35E]
          Length = 626

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/610 (50%), Positives = 419/610 (68%), Gaps = 15/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +   LI+LGKE+GYLT++E+ND LPE + + + IE II+    + I V E   D + ++L
Sbjct: 17   QLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDDDDILL 76

Query: 892  SNITSDDDV--EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            S+  SDDD+  +EA  A L++V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEE
Sbjct: 77   SDTGSDDDIATDEAA-AVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAKRIEE 135

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIK---G 1003
            G +++ + ++  P T+  +L    ++   E KI +IV G +   D +F  N   I+   G
Sbjct: 136  GTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIVSGFLNGDDGDFILNEEEIELDLG 195

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +    ++    E   +D  TE  +         E  ++F  I   +D  ++A  K G  S
Sbjct: 196  SPKTTDKDDAEEDGESD-GTELDDTDDSSLDPEEVRVRFEEIQRLYDVAQEALAKHGRGS 254

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            E+   A++ ++N  + I+   +  +++   +R     V   E++I+++V+    MP   F
Sbjct: 255  EAVKVAYDELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEF 314

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
             K FP NE NL W+ +  K    +   L +  P +  LQQKL+  +  + + + D++ + 
Sbjct: 315  KKTFPSNETNLEWLSHRIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVA 374

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 375  RQMAIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 434

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P  
Sbjct: 435  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEE 494

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P + A    +R 
Sbjct: 495  LGERLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLRE 554

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +++L++LT RE+KVL+MRFGI+M SDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 555  ATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 614

Query: 1419 RYYKLKIFLE 1428
            R   L+ FLE
Sbjct: 615  RSEHLRSFLE 624



 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/597 (49%), Positives = 410/597 (68%), Gaps = 15/597 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +   LI+LGKE+GYLT++E+ND LPE + + + IE II+    + I V E   D + ++L
Sbjct: 17  QLGALIRLGKEQGYLTYAEVNDQLPESVTESDQIEDIIQMLTDVGIQVFEVAPDDDDILL 76

Query: 102 SNITSDDDV--EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           S+  SDDD+  +EA  A L++V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEE
Sbjct: 77  SDTGSDDDIATDEAA-AVLASVETEPGRTTDPVRMYMREMGTVDLLTREGEIGIAKRIEE 135

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIK---G 213
           G +++ + ++  P T+  +L    ++   E KI +IV G +   D +F  N   I+   G
Sbjct: 136 GTREVQYIMAYWPGTVKFVLDEYQQVLLGEKKISDIVSGFLNGDDGDFILNEEEIELDLG 195

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNS 268
           +    ++    E   +D  TE  +         E  ++F  I   +D  ++A  K G  S
Sbjct: 196 SPKTTDKDDAEEDGESD-GTELDDTDDSSLDPEEVRVRFEEIQRLYDVAQEALAKHGRGS 254

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           E+   A++ ++N  + I+   +  +++   +R     V   E++I+++V+    MP   F
Sbjct: 255 EAVKVAYDELANHFMLIKLNNRLSDQVMSLMREVYEDVRSNERRIMKLVIRHGKMPMDEF 314

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
            K FP NE NL W+ +  K    +   L +  P +  LQQKL+  +  + + + D++ + 
Sbjct: 315 KKTFPSNETNLEWLSHRIKGGPAFAETLAKIEPEVVALQQKLLAHEQALQMDIRDMKAVA 374

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 375 RQMAIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 434

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P  
Sbjct: 435 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPEE 494

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P + A    +R 
Sbjct: 495 LGERLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTISSPIENATAEGLRE 554

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +++L++LT RE+KVL+MRFGI+M SDHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 ATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611


>gi|192362484|ref|YP_001981272.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
            Ueda107]
 gi|190688649|gb|ACE86327.1| transcription initiation factor sigma 70 [Cellvibrio japonicus
            Ueda107]
          Length = 633

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/624 (49%), Positives = 431/624 (69%), Gaps = 13/624 (2%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            I S   ++++  + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I
Sbjct: 9    IGSRMSDDVQQQQSRIKELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGI 68

Query: 878  SVSEHVLDTETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
             V E   D +TL++++    +D+       AAL  V+++ GRT DP++MYMREMG+VELL
Sbjct: 69   RVYETAPDADTLLMTDGDAAADEIAAAEAAAALVAVETETGRTTDPVRMYMREMGTVELL 128

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--- 992
            TR+GEI IAKRIEEG+++++HA++  P  +  +L     ++K E ++ +++ G +D    
Sbjct: 129  TREGEIVIAKRIEEGVRELMHALAYWPGAVEHVLNEYALVAKEERRLADVIIGWLDPIED 188

Query: 993  --NFSSNNR-----VIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHF 1044
              + +S++         GNK   EE+   E   ++   E +  +   E+  +F  +   +
Sbjct: 189  IPSATSDDDTELPVAANGNKKAGEEEDEDEEGGSEDEEEAITGVDPEEARARFEELQKQY 248

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +K  KA  K GY S+   K  N + +     +  A+  + + +  R  +++V + E++++
Sbjct: 249  EKTTKALAKHGYGSKQAEKELNALGDLFKFFKLPARQFDPIYNNAREALDKVRKHERRVM 308

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            ++   K  M R  FIK FP NE N +W+ +  K + +    L   +P+++  QQ+L  ++
Sbjct: 309  DLCTRKAQMQRKTFIKEFPGNETNADWLPDLLKGKIEGADKLQVVLPNVQAEQQQLAQIE 368

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  L L  ++DINR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 369  AESSLSLASIKDINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 428

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SR
Sbjct: 429  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSR 488

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 489  QMLQEMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTI 548

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
            ++P ++A    +    +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 549  ISPVESATMEGLMEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 608

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   L+ FL+
Sbjct: 609  QIEAKALRKLRHPSRSDHLRSFLD 632



 Score =  571 bits (1472), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 299/611 (48%), Positives = 422/611 (69%), Gaps = 13/611 (2%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           I S   ++++  + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I
Sbjct: 9   IGSRMSDDVQQQQSRIKELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGI 68

Query: 88  SVSEHVLDTETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
            V E   D +TL++++    +D+       AAL  V+++ GRT DP++MYMREMG+VELL
Sbjct: 69  RVYETAPDADTLLMTDGDAAADEIAAAEAAAALVAVETETGRTTDPVRMYMREMGTVELL 128

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--- 202
           TR+GEI IAKRIEEG+++++HA++  P  +  +L     ++K E ++ +++ G +D    
Sbjct: 129 TREGEIVIAKRIEEGVRELMHALAYWPGAVEHVLNEYALVAKEERRLADVIIGWLDPIED 188

Query: 203 --NFSSNNR-----VIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHF 254
             + +S++         GNK   EE+   E   ++   E +  +   E+  +F  +   +
Sbjct: 189 IPSATSDDDTELPVAANGNKKAGEEEDEDEEGGSEDEEEAITGVDPEEARARFEELQKQY 248

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +K  KA  K GY S+   K  N + +     +  A+  + + +  R  +++V + E++++
Sbjct: 249 EKTTKALAKHGYGSKQAEKELNALGDLFKFFKLPARQFDPIYNNAREALDKVRKHERRVM 308

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           ++   K  M R  FIK FP NE N +W+ +  K + +    L   +P+++  QQ+L  ++
Sbjct: 309 DLCTRKAQMQRKTFIKEFPGNETNADWLPDLLKGKIEGADKLQVVLPNVQAEQQQLAQIE 368

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  L L  ++DINR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 369 AESSLSLASIKDINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 428

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SR
Sbjct: 429 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSR 488

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 489 QMLQEMGREPTPEELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTI 548

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
           ++P ++A    +    +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 549 ISPVESATMEGLMEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 608

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 609 QIEAKALRKLR 619


>gi|381152801|ref|ZP_09864670.1| RNA polymerase sigma factor, sigma-70 family [Methylomicrobium album
            BG8]
 gi|380884773|gb|EIC30650.1| RNA polymerase sigma factor, sigma-70 family [Methylomicrobium album
            BG8]
          Length = 603

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/600 (51%), Positives = 419/600 (69%), Gaps = 16/600 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM--LSN 893
            LI  GK +G+LT++EIND LP DI+D E I+  I     M I V E   D ++L+   + 
Sbjct: 13   LIARGKIQGFLTYAEINDHLPSDIVDPEQIDDFIGMINDMGIQVYEVAPDEDSLITDAAA 72

Query: 894  ITSDD-DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
            +T+DD D EE   AAL++VDS+FGRT DP++MYMREMGSVELLTR  E++IAKRIEEG +
Sbjct: 73   VTTDDEDAEEV--AALASVDSEFGRTTDPVRMYMREMGSVELLTRADELKIAKRIEEGQQ 130

Query: 953  DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++ A++     + + L + + IS +E  I++++++ G  D + + +  V +    + E+
Sbjct: 131  QLVKALARSCVVVDDFLQSYNSISADEGGIRLNDLITGFADYSETDDLSVAQTGAEDVED 190

Query: 1011 KILIESSSADLSTEQLEKLKYESLI-KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 1069
                 ++ AD   E+L+ L  E +  K   +         A +K GY S    +A + ++
Sbjct: 191  -----TAPAD---EELKGLNLEEVSEKVERLRVQLQVATNACKKYGYASAETEQAFDVLA 242

Query: 1070 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 1129
            +  +  ++T + ++K+   +   +  V + E+ IL+I      MPR  FI +F E+E N 
Sbjct: 243  DLFMEFKWTPQYLKKMSGIIPEGVASVREQERIILDICTKHAKMPRPEFIAMFTEDESNP 302

Query: 1130 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 1189
             W+D   +    Y   L  +   +++  + L  ++    L +N L+DINR+M  GE K+R
Sbjct: 303  VWLDRCLEEGSKYAEALKPHEKELRKAIKALGEIEAKFGLTINGLKDINRRMSIGEAKSR 362

Query: 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249
            +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 363  RAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 422

Query: 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 1309
            WIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A++MEMPE+K
Sbjct: 423  WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAVRMEMPEDK 482

Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
            +RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P ++A  A +R   +++L  LT 
Sbjct: 483  VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSRVLSPVESATIAGLRESTQNVLAGLTA 542

Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ FL+G
Sbjct: 543  REAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRCFLDG 602



 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 302/586 (51%), Positives = 408/586 (69%), Gaps = 16/586 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM--LSN 103
           LI  GK +G+LT++EIND LP DI+D E I+  I     M I V E   D ++L+   + 
Sbjct: 13  LIARGKIQGFLTYAEINDHLPSDIVDPEQIDDFIGMINDMGIQVYEVAPDEDSLITDAAA 72

Query: 104 ITSDD-DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
           +T+DD D EE   AAL++VDS+FGRT DP++MYMREMGSVELLTR  E++IAKRIEEG +
Sbjct: 73  VTTDDEDAEEV--AALASVDSEFGRTTDPVRMYMREMGSVELLTRADELKIAKRIEEGQQ 130

Query: 163 DMIHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++ A++     + + L + + IS +E  I++++++ G  D + + +  V +    + E+
Sbjct: 131 QLVKALARSCVVVDDFLQSYNSISADEGGIRLNDLITGFADYSETDDLSVAQTGAEDVED 190

Query: 221 KILIESSSADLSTEQLEKLKYESLI-KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 279
                ++ AD   E+L+ L  E +  K   +         A +K GY S    +A + ++
Sbjct: 191 -----TAPAD---EELKGLNLEEVSEKVERLRVQLQVATNACKKYGYASAETEQAFDVLA 242

Query: 280 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 339
           +  +  ++T + ++K+   +   +  V + E+ IL+I      MPR  FI +F E+E N 
Sbjct: 243 DLFMEFKWTPQYLKKMSGIIPEGVASVREQERIILDICTKHAKMPRPEFIAMFTEDESNP 302

Query: 340 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 399
            W+D   +    Y   L  +   +++  + L  ++    L +N L+DINR+M  GE K+R
Sbjct: 303 VWLDRCLEEGSKYAEALKPHEKELRKAIKALGEIEAKFGLTINGLKDINRRMSIGEAKSR 362

Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
           +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 363 RAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 422

Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
           WIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A++MEMPE+K
Sbjct: 423 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAVRMEMPEDK 482

Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
           +RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P ++A  A +R   +++L  LT 
Sbjct: 483 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSRVLSPVESATIAGLRESTQNVLAGLTA 542

Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 REAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 588


>gi|33519536|ref|NP_878368.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
 gi|33517199|emb|CAD83581.1| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus]
          Length = 617

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 306/612 (50%), Positives = 424/612 (69%), Gaps = 11/612 (1%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLTFSE+ND LPEDIID + + +II+    M I V E   D++
Sbjct: 4    NPQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIIDSDQLNNIIQMMNDMGIQVMEEAPDSD 63

Query: 888  TLMLSN--ITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
              +L+    TS++D E+ATEAA   LS VD+D GRT DP++MYM+EMG+VELLTR+GEI+
Sbjct: 64   DFLLTENCGTSNNDEEDATEAAVQALSHVDTDLGRTTDPVRMYMKEMGAVELLTREGEID 123

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE+G+  +  +++  P  I  +L    ++   E+++ ++V G ++ N   +    K
Sbjct: 124  IAKRIEDGIHQVQCSVAEYPEAITYLLEQYKRVKTGEVRLSDLVTGFVELNLEHDTLSTK 183

Query: 1003 GNKNNNEEKILIESS---SADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGY 1056
               +      +I S      + +TE  +    +  +   KF+++   ++K R   +  G 
Sbjct: 184  TIHDGYITPEIINSPIIIDDEENTENDDDNNVDPELARKKFTDLQKQYEKTRITIKYNGR 243

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +    +     +S      R   K  + L + +R+ ++++   E+ I+++ V+   MP+ 
Sbjct: 244  DHHQSLLEILKLSEVFKQFRLVPKQFDYLVNNMRSMMDRIRLQERLIMKLCVDVSQMPKK 303

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI +F  NE + +W++    +   ++  L      I++   +L  ++ +  L +  +++
Sbjct: 304  KFINLFSGNETSKDWLNKALSLNTSWSQKLHNVDSKIQQSLYQLHQIEKETGLTIEQIKN 363

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            IN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364  INKRMAIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQILQETG EP P
Sbjct: 424  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQILQETGCEPTP 483

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M M E+KIRK++KIAKEPVSME+P+GDDEDSHLGDFIED N+  P D+A + ++
Sbjct: 484  EELAERMFMSEDKIRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNL 543

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+   D+L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 544  RAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 603

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 604  PSRSEILKSFLD 615



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/599 (49%), Positives = 415/599 (69%), Gaps = 11/599 (1%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLTFSE+ND LPEDIID + + +II+    M I V E   D++
Sbjct: 4   NPQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIIDSDQLNNIIQMMNDMGIQVMEEAPDSD 63

Query: 98  TLMLSN--ITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
             +L+    TS++D E+ATEAA   LS VD+D GRT DP++MYM+EMG+VELLTR+GEI+
Sbjct: 64  DFLLTENCGTSNNDEEDATEAAVQALSHVDTDLGRTTDPVRMYMKEMGAVELLTREGEID 123

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE+G+  +  +++  P  I  +L    ++   E+++ ++V G ++ N   +    K
Sbjct: 124 IAKRIEDGIHQVQCSVAEYPEAITYLLEQYKRVKTGEVRLSDLVTGFVELNLEHDTLSTK 183

Query: 213 GNKNNNEEKILIESS---SADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGY 266
              +      +I S      + +TE  +    +  +   KF+++   ++K R   +  G 
Sbjct: 184 TIHDGYITPEIINSPIIIDDEENTENDDDNNVDPELARKKFTDLQKQYEKTRITIKYNGR 243

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +    +     +S      R   K  + L + +R+ ++++   E+ I+++ V+   MP+ 
Sbjct: 244 DHHQSLLEILKLSEVFKQFRLVPKQFDYLVNNMRSMMDRIRLQERLIMKLCVDVSQMPKK 303

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI +F  NE + +W++    +   ++  L      I++   +L  ++ +  L +  +++
Sbjct: 304 KFINLFSGNETSKDWLNKALSLNTSWSQKLHNVDSKIQQSLYQLHQIEKETGLTIEQIKN 363

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           IN++M  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364 INKRMAIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQILQETG EP P
Sbjct: 424 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQILQETGCEPTP 483

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M M E+KIRK++KIAKEPVSME+P+GDDEDSHLGDFIED N+  P D+A + ++
Sbjct: 484 EELAERMFMSEDKIRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPLDSATSDNL 543

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+   D+L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 RAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|419955718|ref|ZP_14471842.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri TS44]
 gi|387967523|gb|EIK51824.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri TS44]
          Length = 618

 Score =  585 bits (1509), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/608 (50%), Positives = 419/608 (68%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN-----------RV 1000
            ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +                + 
Sbjct: 130  REVMSAIAHFPGTVDGILADYERVTTEGGRLSDILSGYIDPDDDGAAGAPPEVEPVAPQA 189

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
                  ++++    + S ++            + ++F  ++    K +KA +K G  S+ 
Sbjct: 190  AAKPAADDKDDDEEDESESEEEEGDGGPDPEVARVRFGAVAEQLQKAKKALKKHGRASQQ 249

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I     ++   + I+   K  + L   +R+ ++Q+   E+ ++++ V    MPR  F++
Sbjct: 250  AIDELEALAVLFMPIKLVPKQYDALVVRVRDALSQIRAQERAVMQLCVRDARMPRADFLR 309

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             FP NE NL W +     +  Y   +      I+  QQKLI L+T+  L + D++DINR+
Sbjct: 310  QFPSNETNLAWAEELAGGKGKYAEAIGARKEDIQRCQQKLIELETECELAIADIKDINRR 369

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 370  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 429

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 430  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 489

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 490  ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEAT 549

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R 
Sbjct: 550  REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 609

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 610  EHLRSFLD 617



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 304/595 (51%), Positives = 410/595 (68%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI+ G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIQRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFEVAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN-----------RV 210
           ++++ AI+  P T+  IL   ++++    ++ +I+ G ID +                + 
Sbjct: 130 REVMSAIAHFPGTVDGILADYERVTTEGGRLSDILSGYIDPDDDGAAGAPPEVEPVAPQA 189

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
                 ++++    + S ++            + ++F  ++    K +KA +K G  S+ 
Sbjct: 190 AAKPAADDKDDDEEDESESEEEEGDGGPDPEVARVRFGAVAEQLQKAKKALKKHGRASQQ 249

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I     ++   + I+   K  + L   +R+ ++Q+   E+ ++++ V    MPR  F++
Sbjct: 250 AIDELEALAVLFMPIKLVPKQYDALVVRVRDALSQIRAQERAVMQLCVRDARMPRADFLR 309

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            FP NE NL W +     +  Y   +      I+  QQKLI L+T+  L + D++DINR+
Sbjct: 310 QFPSNETNLAWAEELAGGKGKYAEAIGARKEDIQRCQQKLIELETECELAIADIKDINRR 369

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 370 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 429

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 430 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 489

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 490 ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAMQSPIDVATVESLKEAT 549

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|238782836|ref|ZP_04626865.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
 gi|238716259|gb|EEQ08242.1| RNA polymerase sigma factor rpoD [Yersinia bercovieri ATCC 43970]
          Length = 612

 Score =  585 bits (1508), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/610 (50%), Positives = 415/610 (68%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N +  +      
Sbjct: 123  KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E              ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 182  HVGSELSTEEMDDDDKEEEDEEEEEDDNSIDPELARQKFSELREQYETTRMAIKKNGRSH 241

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242  ATAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302  VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 542  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 601

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 602  RSEVLRSFLD 611



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/597 (50%), Positives = 406/597 (68%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N +  +      
Sbjct: 123 KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E              ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 182 HVGSELSTEEMDDDDKEEEDEEEEEDDNSIDPELARQKFSELREQYETTRMAIKKNGRSH 241

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 242 ATAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 301

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 302 VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 361

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 362 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 421

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 422 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 481

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 482 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 541

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|206576865|ref|YP_002236518.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288933503|ref|YP_003437562.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|290511438|ref|ZP_06550807.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
 gi|206565923|gb|ACI07699.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae 342]
 gi|288888232|gb|ADC56550.1| RNA polymerase, sigma 70 subunit, RpoD [Klebsiella variicola At-22]
 gi|289776431|gb|EFD84430.1| RNA polymerase primary sigma factor [Klebsiella sp. 1_1_55]
          Length = 613

 Score =  585 bits (1508), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 417/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183  SELSQEEMDDDEDEDEDDDADDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 408/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183 SELSQEEMDDDEDEDEDDDADDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|152971991|ref|YP_001337100.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae MGH 78578]
 gi|330003818|ref|ZP_08304768.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
 gi|365140532|ref|ZP_09346587.1| RNA polymerase sigma factor rpoD [Klebsiella sp. 4_1_44FAA]
 gi|378980765|ref|YP_005228906.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae HS11286]
 gi|386036624|ref|YP_005956537.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae KCTC 2242]
 gi|424832463|ref|ZP_18257191.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae Ecl8]
 gi|424931707|ref|ZP_18350079.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp. pneumoniae
            KpQ3]
 gi|425074852|ref|ZP_18477955.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW1]
 gi|425083268|ref|ZP_18486365.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW2]
 gi|425085488|ref|ZP_18488581.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW3]
 gi|425093351|ref|ZP_18496435.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW5]
 gi|428931828|ref|ZP_19005418.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae JHCK1]
 gi|449047215|ref|ZP_21730713.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae hvKP1]
 gi|150956840|gb|ABR78870.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp. pneumoniae
            MGH 78578]
 gi|328536802|gb|EGF63114.1| RNA polymerase sigma factor RpoD [Klebsiella sp. MS 92-3]
 gi|339763752|gb|AEJ99972.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae KCTC 2242]
 gi|363653848|gb|EHL92797.1| RNA polymerase sigma factor rpoD [Klebsiella sp. 4_1_44FAA]
 gi|364520176|gb|AEW63304.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae HS11286]
 gi|405595055|gb|EKB68445.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW1]
 gi|405599587|gb|EKB72763.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW2]
 gi|405607520|gb|EKB80489.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW3]
 gi|405610896|gb|EKB83685.1| RNA polymerase sigma factor rpoD [Klebsiella pneumoniae subsp.
            pneumoniae WGLW5]
 gi|407805894|gb|EKF77145.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp. pneumoniae
            KpQ3]
 gi|414709905|emb|CCN31609.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae Ecl8]
 gi|426307762|gb|EKV69838.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae JHCK1]
 gi|448877467|gb|EMB12431.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae hvKP1]
          Length = 613

 Score =  585 bits (1508), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 417/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183  SELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 408/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   E  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183 SELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|238896571|ref|YP_002921314.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae NTUH-K2044]
 gi|402778931|ref|YP_006634477.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae 1084]
 gi|419764769|ref|ZP_14291008.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae DSM 30104]
 gi|238548896|dbj|BAH65247.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp. pneumoniae
            NTUH-K2044]
 gi|397741897|gb|EJK89116.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae DSM 30104]
 gi|402539880|gb|AFQ64029.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
            pneumoniae 1084]
          Length = 632

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 305/619 (49%), Positives = 420/619 (67%), Gaps = 8/619 (1%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 13   IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 72

Query: 878  SVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
             V E   D + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR
Sbjct: 73   QVMEEAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTR 132

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +
Sbjct: 133  EGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEED 192

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRK 1049
                  +  +   +  ++    +   E  +    +        +  KF+ +   ++  R 
Sbjct: 193  MAPTATHVGSELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRD 252

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              + +G +  +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 253  TIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVE 312

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +C MP+ +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L
Sbjct: 313  QCKMPKKNFITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGL 372

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 373  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 432

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 433  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 492

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 493  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 552

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 553  SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 612

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 613  ALRKLRHPSRSEVLRSFLD 631



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/606 (49%), Positives = 411/606 (67%), Gaps = 8/606 (1%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           IK   R   +N + + K+L++ GKE+GYLT++E+ND LPEDI+D + IE II+    M I
Sbjct: 13  IKCGYRLMEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGI 72

Query: 88  SVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
            V E   D + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR
Sbjct: 73  QVMEEAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTR 132

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEI+IAKRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +
Sbjct: 133 EGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEED 192

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRK 259
                 +  +   +  ++    +   E  +    +        +  KF+ +   ++  R 
Sbjct: 193 MAPTATHVGSELSQEEMDDDEDEDEDEDADDNSDDDNSIDPELAREKFAELRTQYELTRD 252

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             + +G +  +  +    +S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 253 TIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVE 312

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +C MP+ +FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L
Sbjct: 313 QCKMPKKNFITLFTGNETSETWFNAAVAMNKPWSEKLLEVKEDVQRGLQKLQQIEEETGL 372

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 373 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 432

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 433 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 492

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 493 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 552

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A   S+R+   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 553 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 612

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 613 ALRKLR 618


>gi|422015788|ref|ZP_16362381.1| RNA polymerase sigma factor RpoD [Providencia burhodogranariea DSM
            19968]
 gi|414096502|gb|EKT58159.1| RNA polymerase sigma factor RpoD [Providencia burhodogranariea DSM
            19968]
          Length = 617

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 310/628 (49%), Positives = 418/628 (66%), Gaps = 40/628 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI----------------------KFSNI 1040
                EE +   ++   ++L  E+L K + E                         KF  +
Sbjct: 172  ---AEEDLAPTATHVGSELPQEELNKDEDEDEEDEDGDDSDSDDDNSIDPELAREKFGEL 228

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
               ++K R+  ++ G ++     A   +S      R   K  + L + +R  +++V   E
Sbjct: 229  REQYEKTRQHIKQFGRSNAQTAIAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQE 288

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + I+++ V +C MP+ +FI +F  NE +  W+     +   ++  L      I    Q+L
Sbjct: 289  RTIMKLCVEQCKMPKKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRL 348

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
              ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 349  RQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 408

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 409  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 468

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIE
Sbjct: 469  RISRQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIE 528

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D  +  P D+A + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 529  DTTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 588

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  ERIRQIEAKALRKLRHPSRSEVLRSFLD 616



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/615 (49%), Positives = 409/615 (66%), Gaps = 40/615 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI----------------------KFSNI 250
               EE +   ++   ++L  E+L K + E                         KF  +
Sbjct: 172 ---AEEDLAPTATHVGSELPQEELNKDEDEDEEDEDGDDSDSDDDNSIDPELAREKFGEL 228

Query: 251 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
              ++K R+  ++ G ++     A   +S      R   K  + L + +R  +++V   E
Sbjct: 229 REQYEKTRQHIKQFGRSNAQTAIAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQE 288

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           + I+++ V +C MP+ +FI +F  NE +  W+     +   ++  L      I    Q+L
Sbjct: 289 RTIMKLCVEQCKMPKKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRL 348

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
             ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 349 RQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 408

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 409 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 468

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIE
Sbjct: 469 RISRQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIE 528

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D  +  P D+A + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 529 DTTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 588

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 589 ERIRQIEAKALRKLR 603


>gi|157372533|ref|YP_001480522.1| RNA polymerase sigma factor RpoD [Serratia proteamaculans 568]
 gi|157324297|gb|ABV43394.1| RNA polymerase, sigma 70 subunit, RpoD [Serratia proteamaculans 568]
          Length = 647

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 419/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 98

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 159  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 218

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ + EE+   E    +   E    +  E +  KF+++   ++  R   +K G +  S
Sbjct: 219  VGSELSTEEQKDDEEEDDEDEEEDDNSIDPELARQKFADLRDQYEATRVVIKKNGRSHAS 278

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 279  AAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVT 338

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 339  LFSSNETSDTWFAAALAMAKPWSEKLKDVADDVQRSLQKLRQIEEETGLTIEQVKDINRR 398

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 399  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 458

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 459  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 518

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 519  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 578

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 579  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 638

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 639  EVLRSFLD 646



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 410/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 39  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 98

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 99  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 158

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 159 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 218

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ + EE+   E    +   E    +  E +  KF+++   ++  R   +K G +  S
Sbjct: 219 VGSELSTEEQKDDEEEDDEDEEEDDNSIDPELARQKFADLRDQYEATRVVIKKNGRSHAS 278

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 279 AAEEILKLSEVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKNFVT 338

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 339 LFSSNETSDTWFAAALAMAKPWSEKLKDVADDVQRSLQKLRQIEEETGLTIEQVKDINRR 398

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 399 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 458

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 459 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 518

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 519 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 578

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 579 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 633


>gi|383935444|ref|ZP_09988880.1| RNA polymerase primary sigma factor [Rheinheimera nanhaiensis E407-8]
 gi|383703538|dbj|GAB58971.1| RNA polymerase primary sigma factor [Rheinheimera nanhaiensis E407-8]
          Length = 614

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/623 (49%), Positives = 410/623 (65%), Gaps = 33/623 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + L++S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLIMSDATTDEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   DK    EI++ +IV   ID N            +
Sbjct: 123  IEDGINTVQSSVAEYPEAITYLLEQWDKYEAEEIRLSDIVTAFIDPN------------D 170

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFHFD 1045
             +E  I      +D+  +QL+                             KF+ +   +D
Sbjct: 171  IDEAPIAGSHIGSDVPEDQLDDDDDSDDDDDSDGDSDDGDSGPDPEMARQKFAELRTQYD 230

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
              R +  + G    +       +S      R   K  ++L   +R  +++V   E+ +++
Sbjct: 231  ITRNSIVQNGREHATTKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERIVMK 290

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V    MP+ +F+K F   E +  W+D E   +  Y+  L  +   +    +KL  ++ 
Sbjct: 291  HCVEYAKMPKKNFVKAFTGFETSTAWLDAEIAAKKPYSEKLDEHKDELVRSIEKLKKIEE 350

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
            +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 351  ETGLSIFKIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 410

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 411  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 470

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G EP P  ++ +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  
Sbjct: 471  MLQEMGREPSPEELSERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGE 530

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 531  SPLDSATMESLKNATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 590

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   LK FL+
Sbjct: 591  IEAKALRKLRHPSRSEVLKSFLD 613



 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 401/610 (65%), Gaps = 33/610 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFESAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + L++S+ T+D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLIMSDATTDEDAVEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   DK    EI++ +IV   ID N            +
Sbjct: 123 IEDGINTVQSSVAEYPEAITYLLEQWDKYEAEEIRLSDIVTAFIDPN------------D 170

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFHFD 255
            +E  I      +D+  +QL+                             KF+ +   +D
Sbjct: 171 IDEAPIAGSHIGSDVPEDQLDDDDDSDDDDDSDGDSDDGDSGPDPEMARQKFAELRTQYD 230

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
             R +  + G    +       +S      R   K  ++L   +R  +++V   E+ +++
Sbjct: 231 ITRNSIVQNGREHATTKTEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERIVMK 290

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V    MP+ +F+K F   E +  W+D E   +  Y+  L  +   +    +KL  ++ 
Sbjct: 291 HCVEYAKMPKKNFVKAFTGFETSTAWLDAEIAAKKPYSEKLDEHKDELVRSIEKLKKIEE 350

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
           +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 351 ETGLSIFKIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 410

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 411 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 470

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G EP P  ++ +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +  
Sbjct: 471 MLQEMGREPSPEELSERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSSGE 530

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 531 SPLDSATMESLKNATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 590

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 591 IEAKALRKLR 600


>gi|188532569|ref|YP_001906366.1| RNA polymerase sigma factor RpoD [Erwinia tasmaniensis Et1/99]
 gi|188027611|emb|CAO95461.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia tasmaniensis
            Et1/99]
          Length = 613

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/610 (50%), Positives = 412/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAINYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +       E    D  ++        S+       KFS++   ++  R   + +  + 
Sbjct: 183  VGSELSAEEREDDDEDEESDDDSSDDDNSIDPELAREKFSDLRIQYETTRTVIKAKSRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +F
Sbjct: 243  ADAIVEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERLIMKLCVELCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETNETWFKAALAMNKPWSEKLNDVSEDVTRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/597 (50%), Positives = 403/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAINYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +       E    D  ++        S+       KFS++   ++  R   + +  + 
Sbjct: 183 VGSELSAEEREDDDEDEESDDDSSDDDNSIDPELAREKFSDLRIQYETTRTVIKAKSRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +F
Sbjct: 243 ADAIVEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERLIMKLCVELCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETNETWFKAALAMNKPWSEKLNDVSEDVTRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|238762467|ref|ZP_04623438.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
 gi|238699452|gb|EEP92198.1| RNA polymerase sigma factor rpoD [Yersinia kristensenii ATCC 33638]
          Length = 613

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 308/610 (50%), Positives = 415/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ ++++G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
              +       +        ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 183  VGSELSTEERDDDDDKEDEDEEEEEDDNSIDPELARQKFSELREQYENTRMAIKKNGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             S      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ASAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303  VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/597 (50%), Positives = 406/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ ++++G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
             +       +        ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 183 VGSELSTEERDDDDDKEDEDEEEEEDDNSIDPELARQKFSELREQYENTRMAIKKNGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            S      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ASAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303 VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|238796946|ref|ZP_04640450.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
 gi|238719206|gb|EEQ11018.1| RNA polymerase sigma factor rpoD [Yersinia mollaretii ATCC 43969]
          Length = 634

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/610 (50%), Positives = 415/610 (68%), Gaps = 9/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 84

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 85   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 144

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N +  +      
Sbjct: 145  KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN-AEEDIAPTAT 203

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E              ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 204  HVGSELSTEEMDDDDKEEEDEEEEEDDNSIDPELARQKFSELREQYENTRMAIKKNGRSH 263

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 264  ATAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 323

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 324  VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 383

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 384  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 443

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 444  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 503

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 504  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 563

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 564  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 623

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 624  RSEVLRSFLD 633



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/597 (50%), Positives = 406/597 (68%), Gaps = 9/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 25  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 84

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 85  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 144

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P  I  +L   D++   E ++ ++++G +D N +  +      
Sbjct: 145 KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN-AEEDIAPTAT 203

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E              ++ E+    S+       KFS +   ++  R A +K G + 
Sbjct: 204 HVGSELSTEEMDDDDKEEEDEEEEEDDNSIDPELARQKFSELREQYENTRMAIKKNGRSH 263

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +      N+S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 264 ATAAAEILNLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKKNF 323

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 324 VTLFASNETSDTWFAAAVAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTIEQVKDIN 383

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 384 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 443

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 444 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 503

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 504 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 563

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 564 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 620


>gi|307546061|ref|YP_003898540.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
 gi|307218085|emb|CBV43355.1| RNA polymerase sigma factor RpoD [Halomonas elongata DSM 2581]
          Length = 615

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 311/610 (50%), Positives = 409/610 (67%), Gaps = 18/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+G+LT++E+ND LPEDI D + +E II     M I+V E   D +TLM+
Sbjct: 10   RLKELIARGKEQGFLTYAEVNDHLPEDIADPDQVEDIIGMINDMGINVVEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            ++ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   ADQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ A++  P  +  IL A D     E   ++ ++  G ID +       I G    + 
Sbjct: 130  REVMSALAYLPGAVDSILEAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEADV 184

Query: 1010 EKILIESSSADLSTEQLEKLKY-----------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             +   E S+AD      +               E+  +F  I    +  R+A E+ G  +
Sbjct: 185  PEPEPEQSAADGEASDEDDDAEEEESGGGPDPEEARARFEQIREQNEAARRAIEEHGRGA 244

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +        ++     I+   K  E+L   +R  + QV   EK I+++ V K  +PR  F
Sbjct: 245  KQAQDELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEKAIMQLCVKKAKVPRKTF 304

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            IK FP NE   +W+D+       Y   L      I+  Q+K+   +  + L + DL+++N
Sbjct: 305  IKSFPGNESRQDWLDSFMAENAKYADRLAPLKGDIQRAQRKIAFEEEMVALVVTDLKEVN 364

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            RK+  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 365  RKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 424

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 425  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 484

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  M+ P D+A    +  
Sbjct: 485  LGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMVLPIDSATGEGLIE 544

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 545  ATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 604

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 605  RSEPLRSFLD 614



 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 304/597 (50%), Positives = 400/597 (67%), Gaps = 18/597 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+G+LT++E+ND LPEDI D + +E II     M I+V E   D +TLM+
Sbjct: 10  RLKELIARGKEQGFLTYAEVNDHLPEDIADPDQVEDIIGMINDMGINVVEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           ++ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  ADQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ A++  P  +  IL A D     E   ++ ++  G ID +       I G    + 
Sbjct: 130 REVMSALAYLPGAVDSILEAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEADV 184

Query: 220 EKILIESSSADLSTEQLEKLKY-----------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
            +   E S+AD      +               E+  +F  I    +  R+A E+ G  +
Sbjct: 185 PEPEPEQSAADGEASDEDDDAEEEESGGGPDPEEARARFEQIREQNEAARRAIEEHGRGA 244

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +        ++     I+   K  E+L   +R  + QV   EK I+++ V K  +PR  F
Sbjct: 245 KQAQDELARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEKAIMQLCVKKAKVPRKTF 304

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           IK FP NE   +W+D+       Y   L      I+  Q+K+   +  + L + DL+++N
Sbjct: 305 IKSFPGNESRQDWLDSFMAENAKYADRLAPLKGDIQRAQRKIAFEEEMVALVVTDLKEVN 364

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           RK+  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 365 RKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 424

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 425 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 484

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  M+ P D+A    +  
Sbjct: 485 LGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMVLPIDSATGEGLIE 544

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 ATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|259907100|ref|YP_002647456.1| RNA polymerase sigma factor RpoD [Erwinia pyrifoliae Ep1/96]
 gi|385787029|ref|YP_005818138.1| RNA polymerase sigma factor RpoD [Erwinia sp. Ejp617]
 gi|387869818|ref|YP_005801188.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia pyrifoliae DSM
            12163]
 gi|224962722|emb|CAX54177.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia pyrifoliae
            Ep1/96]
 gi|283476901|emb|CAY72757.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia pyrifoliae DSM
            12163]
 gi|310766301|gb|ADP11251.1| RNA polymerase sigma factor RpoD [Erwinia sp. Ejp617]
          Length = 613

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 307/610 (50%), Positives = 411/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +       E    D  ++        S+       KF ++   ++  R   + +  + 
Sbjct: 183  VGSELSAEEREDEDEDEESDDDSSDDDNSIDPELAREKFGDLRIQYETTRTVIKAKSRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +F
Sbjct: 243  ADAIAEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETNETWFKAALAMNKPWSEKLNDVSDDVNRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/597 (50%), Positives = 402/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +       E    D  ++        S+       KF ++   ++  R   + +  + 
Sbjct: 183 VGSELSAEEREDEDEDEESDDDSSDDDNSIDPELAREKFGDLRIQYETTRTVIKAKSRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +F
Sbjct: 243 ADAIAEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETNETWFKAALAMNKPWSEKLNDVSDDVNRGLQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|422007703|ref|ZP_16354689.1| RNA polymerase sigma factor RpoD [Providencia rettgeri Dmel1]
 gi|414097593|gb|EKT59248.1| RNA polymerase sigma factor RpoD [Providencia rettgeri Dmel1]
          Length = 617

 Score =  584 bits (1506), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 304/614 (49%), Positives = 415/614 (67%), Gaps = 12/614 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
              +   +  ++ +  +   ++                    KFS++   ++K R+  ++ 
Sbjct: 183  VGSELPQEELDKNDDEDEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRQHIKQY 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +      A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243  GRSDAKTAAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            + +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +  +
Sbjct: 303  KKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483  SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 603  RHPSRSEVLRSFLD 616



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 297/601 (49%), Positives = 406/601 (67%), Gaps = 12/601 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
             +   +  ++ +  +   ++                    KFS++   ++K R+  ++ 
Sbjct: 183 VGSELPQEELDKNDDEDEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRQHIKQY 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +      A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243 GRSDAKTAAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           + +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +  +
Sbjct: 303 KKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483 SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|268590608|ref|ZP_06124829.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
 gi|291314000|gb|EFE54453.1| RNA polymerase sigma factor RpoD [Providencia rettgeri DSM 1131]
          Length = 617

 Score =  584 bits (1506), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 304/614 (49%), Positives = 414/614 (67%), Gaps = 12/614 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
              +   +  ++    +   ++                    KFS++   ++K R+  ++ 
Sbjct: 183  VGSELPQEELDKDDDEDEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRQHIKQY 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +      A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243  GRSDAKTAAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            + +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +  +
Sbjct: 303  KKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483  SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 603  RHPSRSEVLRSFLD 616



 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 297/601 (49%), Positives = 405/601 (67%), Gaps = 12/601 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
             +   +  ++    +   ++                    KFS++   ++K R+  ++ 
Sbjct: 183 VGSELPQEELDKDDDEDEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRQHIKQY 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +      A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP
Sbjct: 243 GRSDAKTAAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           + +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +  +
Sbjct: 303 KKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTIEQV 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483 SPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|212711167|ref|ZP_03319295.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
            30120]
 gi|422019957|ref|ZP_16366499.1| RNA polymerase sigma factor RpoD [Providencia alcalifaciens Dmel2]
 gi|212686335|gb|EEB45863.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
            30120]
 gi|414102581|gb|EKT64173.1| RNA polymerase sigma factor RpoD [Providencia alcalifaciens Dmel2]
          Length = 615

 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 416/612 (67%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +   +  ++    +   +  +    +        +  KFS++   ++K R   ++ G 
Sbjct: 183  VGSELPQEELDDDEEEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRTHIKQYGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +    + A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243  SDAKTVAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  NE +  W+     +   ++  L      +    Q+L  ++ +  L +  ++D
Sbjct: 303  NFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEVLRCLQRLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 407/599 (67%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAENTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +   +  ++    +   +  +    +        +  KFS++   ++K R   ++ G 
Sbjct: 183 VGSELPQEELDDDEEEEDEDGDDSDSDDDNSIDPELARQKFSDLREQYEKTRTHIKQYGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +    + A   +S      R   K  + L + +R  +++V   E+ I+++ V +C MP+ 
Sbjct: 243 SDAKTVAAIEQLSEVFKEFRLVPKQFDYLVNNMREMMDRVRLQERTIMKLCVEQCKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  NE +  W+     +   ++  L      +    Q+L  ++ +  L +  ++D
Sbjct: 303 NFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEVLRCLQRLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|354599220|ref|ZP_09017237.1| RNA polymerase, sigma 70 subunit, RpoD [Brenneria sp. EniD312]
 gi|353677155|gb|EHD23188.1| RNA polymerase, sigma 70 subunit, RpoD [Brenneria sp. EniD312]
          Length = 611

 Score =  584 bits (1506), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 422/608 (69%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ +++E    E    D  ++    +  E +  KF+++   ++  R+  +  G +   
Sbjct: 183  VGSELSSKEIEDDEEEEDDDDSDDDNSIDPELARQKFNDLREQYETTRQVIKANGRSHAK 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243  SAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N +W      +   ++  L      +K   QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFSGNETNDSWFIAAIAMSKPWSEKLHEVEDDVKRSLQKLHQVEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 413/595 (69%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ +++E    E    D  ++    +  E +  KF+++   ++  R+  +  G +   
Sbjct: 183 VGSELSSKEIEDDEEEEDDDDSDDDNSIDPELARQKFNDLREQYETTRQVIKANGRSHAK 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243 SAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIMKLCVEQCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N +W      +   ++  L      +K   QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFSGNETNDSWFIAAIAMSKPWSEKLHEVEDDVKRSLQKLHQVEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|262275021|ref|ZP_06052832.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
 gi|262221584|gb|EEY72898.1| RNA polymerase sigma factor RpoD [Grimontia hollisae CIP 101886]
          Length = 615

 Score =  584 bits (1505), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/612 (50%), Positives = 424/612 (69%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM+S   +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMSETVADEDAVEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKG 1003
            IE+G+  +  +++  P +I  +L   DK+   E+++ +I+ G +D N    +     I  
Sbjct: 123  IEDGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDIISGFVDPNQDDIAPTATHIGS 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGY 1056
               + +     +    D   +  ++ + ++ I       KF+ +   ++ M+++ +K G 
Sbjct: 183  ELTDEQLDDEDDDVDDDDDEDSEDEAEEDTGIDPELAREKFNELRVAYEGMQQSIQKYGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              E    A   +S      R   K  ++L + +R+ +++V   E+ I+ + V++  MP+ 
Sbjct: 243  FHEQTTVAIAELSEVFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIIMRLCVDQAKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+++F  NE +  W+D        Y   L ++   ++   QKL  ++ +  L +  ++D
Sbjct: 303  TFVQLFAGNESSDAWLDKALASDKPYAERLKQHEEDLRRCIQKLKIVEDETGLSVERVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  ISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   ++
Sbjct: 483  EELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPMDSATMNNL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  KMATSEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/599 (50%), Positives = 415/599 (69%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM+S   +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMSETVADEDAVEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKG 213
           IE+G+  +  +++  P +I  +L   DK+   E+++ +I+ G +D N    +     I  
Sbjct: 123 IEDGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDIISGFVDPNQDDIAPTATHIGS 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGY 266
              + +     +    D   +  ++ + ++ I       KF+ +   ++ M+++ +K G 
Sbjct: 183 ELTDEQLDDEDDDVDDDDDEDSEDEAEEDTGIDPELAREKFNELRVAYEGMQQSIQKYGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             E    A   +S      R   K  ++L + +R+ +++V   E+ I+ + V++  MP+ 
Sbjct: 243 FHEQTTVAIAELSEVFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIIMRLCVDQAKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+++F  NE +  W+D        Y   L ++   ++   QKL  ++ +  L +  ++D
Sbjct: 303 TFVQLFAGNESSDAWLDKALASDKPYAERLKQHEEDLRRCIQKLKIVEDETGLSVERVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 ISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   ++
Sbjct: 483 EELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPMDSATMNNL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 KMATSEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|260773557|ref|ZP_05882473.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
 gi|260612696|gb|EEX37899.1| RNA polymerase sigma factor RpoD [Vibrio metschnikovii CIP 69.14]
          Length = 623

 Score =  584 bits (1505), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 321/627 (51%), Positives = 418/627 (66%), Gaps = 32/627 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDNTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  A++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123  KRIEEGINQVQSAVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNEDETTAPTATH 182

Query: 1005 KNNNEEKILIESSSADLS----------------------TEQLEKLKYE-SLIKFSNIS 1041
                   I  E + ADL                        E+   +  E +L KF+ + 
Sbjct: 183  -------IGSELTGADLDDEDSKDIDEDEDEDEDGDSTDDAEEDTGIDPELALEKFTELR 235

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              +  ++ A  + G +S +  +A   + +     R T K  + L  TLRN + +V   E+
Sbjct: 236  NKYQNLQLAINEHGNDSSTTQQASELVLDIFREFRLTPKQFDHLVTTLRNSMERVRTQER 295

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
             I++ VV    MP+  FI +F  NE +  W+D        Y   +  N   I+   QKL 
Sbjct: 296  LIMKTVVEVAKMPKKSFIALFTGNESSEAWLDQVLATDKPYVEKIRANEEMIRRSIQKLR 355

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++ +  L +N ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 356  IIEQETSLDVNRIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 416  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 475

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 476  ISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 535

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
              +  P D+A   S+R+  +D L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 536  TTLELPLDSATATSLRAATRDALAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 595

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RIRQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 314/614 (51%), Positives = 409/614 (66%), Gaps = 32/614 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDNTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  A++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123 KRIEEGINQVQSAVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNEDETTAPTATH 182

Query: 215 KNNNEEKILIESSSADLS----------------------TEQLEKLKYE-SLIKFSNIS 251
                  I  E + ADL                        E+   +  E +L KF+ + 
Sbjct: 183 -------IGSELTGADLDDEDSKDIDEDEDEDEDGDSTDDAEEDTGIDPELALEKFTELR 235

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
             +  ++ A  + G +S +  +A   + +     R T K  + L  TLRN + +V   E+
Sbjct: 236 NKYQNLQLAINEHGNDSSTTQQASELVLDIFREFRLTPKQFDHLVTTLRNSMERVRTQER 295

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 371
            I++ VV    MP+  FI +F  NE +  W+D        Y   +  N   I+   QKL 
Sbjct: 296 LIMKTVVEVAKMPKKSFIALFTGNESSEAWLDQVLATDKPYVEKIRANEEMIRRSIQKLR 355

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            ++ +  L +N ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 356 IIEQETSLDVNRIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 475

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           ISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 476 ISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIED 535

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
             +  P D+A   S+R+  +D L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 536 TTLELPLDSATATSLRAATRDALAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 595

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 596 RIRQIEAKALRKLR 609


>gi|27364091|ref|NP_759619.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|320157475|ref|YP_004189854.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
 gi|27360209|gb|AAO09146.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus CMCP6]
 gi|319932787|gb|ADV87651.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus MO6-24/O]
          Length = 624

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 318/637 (49%), Positives = 423/637 (66%), Gaps = 53/637 (8%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D +
Sbjct: 4    NPQSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 63

Query: 888  TLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             L LS+ T  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 64   DLALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          + 
Sbjct: 124  RIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNADETAAPTATH- 182

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYE------------------------SLIKFSNIS 1041
                  I  E + +DL  E    +  E                        +L KF+ + 
Sbjct: 183  ------IGSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLR 236

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              +  ++ A  + G  S    +AH  + +     R T K  + L + LR  +++V   E+
Sbjct: 237  NSYQNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQER 296

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---- 1157
             I++  V    MP+  FI +F  NE N  W+D           IL  + P +++++    
Sbjct: 297  LIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQ----------ILASDKPYVEKIKLHEE 346

Query: 1158 ------QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
                   KL  ++ +  L +N+++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 347  DIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 406

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 407  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 466

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDE
Sbjct: 467  MIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDE 526

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED  +  P D+A   S+++  KD+L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 527  DSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 587  VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 623



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 311/624 (49%), Positives = 414/624 (66%), Gaps = 53/624 (8%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D +
Sbjct: 4   NPQSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 63

Query: 98  TLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            L LS+ T  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 64  DLALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 123

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          + 
Sbjct: 124 RIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNADETAAPTATH- 182

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYE------------------------SLIKFSNIS 251
                 I  E + +DL  E    +  E                        +L KF+ + 
Sbjct: 183 ------IGSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLR 236

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
             +  ++ A  + G  S    +AH  + +     R T K  + L + LR  +++V   E+
Sbjct: 237 NSYQNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQER 296

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---- 367
            I++  V    MP+  FI +F  NE N  W+D           IL  + P +++++    
Sbjct: 297 LIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQ----------ILASDKPYVEKIKLHEE 346

Query: 368 ------QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
                  KL  ++ +  L +N+++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 347 DIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 406

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 407 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 466

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDE
Sbjct: 467 MIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDE 526

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED  +  P D+A   S+++  KD+L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 527 DSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKLR
Sbjct: 587 VGKQFDVTRERIRQIEAKALRKLR 610


>gi|335424683|ref|ZP_08553687.1| RNA polymerase, sigma 70 subunit, RpoD [Salinisphaera shabanensis
            E1L3A]
 gi|334888114|gb|EGM26420.1| RNA polymerase, sigma 70 subunit, RpoD [Salinisphaera shabanensis
            E1L3A]
          Length = 622

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/607 (50%), Positives = 418/607 (68%), Gaps = 19/607 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  GK++GYLT++E+ND LP+DI+D E IE I+     M I+V E   + ++L
Sbjct: 26   KSQLRLLIAHGKQKGYLTYAEVNDTLPDDIVDPEQIEDIVNMISDMGITVHESAPEDDSL 85

Query: 890  MLSNITSDDDVEEATEAALSTV---DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            +++  T ++D ++  E A +T+   D  FGRT DP++MYMREMG+VELL R GEI IAKR
Sbjct: 86   LMNENTVNEDDDDDAEEAAATLAALDPQFGRTTDPVRMYMREMGTVELLDRQGEIRIAKR 145

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS---NNRVIKG 1003
            IEEGL +M+ +++  P T   +L    ++  ++ ++ +++ G +D +      N      
Sbjct: 146  IEEGLAEMMFSLAYFPATTGRLLELWSQVESDDKRLTDVLVGFVDPDTGDPIVNEDEAAD 205

Query: 1004 NKNNNEEKILIESSSADL--STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            + N+++E     +   D   +  Q +KLK          S H +      +K G   E+ 
Sbjct: 206  SDNDDDEGSAPSNDGPDPEEAKAQFDKLK----------SLH-EAAVATLDKHGREHEAT 254

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +A N ++   +  +   K+ + L   LR  +  +  IE+++L+I V + GMPR  F++ 
Sbjct: 255  EEALNALATHFMRFKLVPKTADDLTLQLRTTMLDIRSIEREMLQICVTEAGMPRRDFVRQ 314

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
             P+N  +  W+D   + +  Y+  +      +   Q ++  ++++  L +N +++INRKM
Sbjct: 315  LPDNLTSEVWLDKLIRAKRRYSSTIAGRREELVRAQGRIREIESENGLNVNHIKEINRKM 374

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 375  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 434

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A 
Sbjct: 435  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAE 494

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N +AP D+A   S+R    
Sbjct: 495  RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNAVAPDDSASGESLREATH 554

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            + L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 555  NTLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAT 614

Query: 1422 KLKIFLE 1428
             LK FL+
Sbjct: 615  FLKSFLD 621



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 297/594 (50%), Positives = 409/594 (68%), Gaps = 19/594 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  GK++GYLT++E+ND LP+DI+D E IE I+     M I+V E   + ++L
Sbjct: 26  KSQLRLLIAHGKQKGYLTYAEVNDTLPDDIVDPEQIEDIVNMISDMGITVHESAPEDDSL 85

Query: 100 MLSNITSDDDVEEATEAALSTV---DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           +++  T ++D ++  E A +T+   D  FGRT DP++MYMREMG+VELL R GEI IAKR
Sbjct: 86  LMNENTVNEDDDDDAEEAAATLAALDPQFGRTTDPVRMYMREMGTVELLDRQGEIRIAKR 145

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS---NNRVIKG 213
           IEEGL +M+ +++  P T   +L    ++  ++ ++ +++ G +D +      N      
Sbjct: 146 IEEGLAEMMFSLAYFPATTGRLLELWSQVESDDKRLTDVLVGFVDPDTGDPIVNEDEAAD 205

Query: 214 NKNNNEEKILIESSSADL--STEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           + N+++E     +   D   +  Q +KLK          S H +      +K G   E+ 
Sbjct: 206 SDNDDDEGSAPSNDGPDPEEAKAQFDKLK----------SLH-EAAVATLDKHGREHEAT 254

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +A N ++   +  +   K+ + L   LR  +  +  IE+++L+I V + GMPR  F++ 
Sbjct: 255 EEALNALATHFMRFKLVPKTADDLTLQLRTTMLDIRSIEREMLQICVTEAGMPRRDFVRQ 314

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
            P+N  +  W+D   + +  Y+  +      +   Q ++  ++++  L +N +++INRKM
Sbjct: 315 LPDNLTSEVWLDKLIRAKRRYSSTIAGRREELVRAQGRIREIESENGLNVNHIKEINRKM 374

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 375 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 434

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A 
Sbjct: 435 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAE 494

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N +AP D+A   S+R    
Sbjct: 495 RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNAVAPDDSASGESLREATH 554

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           + L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 NTLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608


>gi|335041905|ref|ZP_08534932.1| DNA-directed RNA polymerase, sigma subunit [Methylophaga
            aminisulfidivorans MP]
 gi|333788519|gb|EGL54401.1| DNA-directed RNA polymerase, sigma subunit [Methylophaga
            aminisulfidivorans MP]
          Length = 614

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 301/623 (48%), Positives = 427/623 (68%), Gaps = 29/623 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1    MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 886  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            T+ +  +   ++S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61   TDEMERLAEAVSSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G     F S   +++
Sbjct: 121  IAKRIEAGLRESLMMLSTYPACISSFLELYDAVEAGEMRLNELIKG-----FVSAEELVE 175

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKY---------------ESLIKFSNISFHFDKM 1047
             + + ++         +D  ++  +                   E+ ++F  +   F+  
Sbjct: 176  EHDDLSDTDDDDADDDSDSDSDDDDDDSVDNVSDDDDSGEIDPEEARVRFEALKESFNAY 235

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
             KA   EG  +E+   +    S + +  + T K++  L D +   +N++   E+ I++IV
Sbjct: 236  LKA---EGEEAEA---SREQASAQFMEFKLTPKTLAYLNDLMSETVNEIRNQERIIMDIV 289

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V +  M R  FI  F  NE N+NW D   + +  Y+  + ++   I   Q  L  +    
Sbjct: 290  VEQARMNRRDFIDSFQGNESNVNWADKHIRAKKHYSSTIKKHHDEIIAAQSVLAEIAESR 349

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             + ++++++I+R+M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 350  GMSISEIKEISRQMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 409

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEY+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+L
Sbjct: 410  LMKAVDKFEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQML 469

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +++MPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P
Sbjct: 470  QEMGREPTPDELAERVDMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISP 529

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
            SD+A+   +R   + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 530  SDSAIIEGLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 589

Query: 1408 AKALRKLRHPSRYYKLKIFLEGK 1430
            AKALRKLRHPSR  +L+ FL+ +
Sbjct: 590  AKALRKLRHPSRSDQLRSFLDSE 612



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 297/616 (48%), Positives = 419/616 (68%), Gaps = 30/616 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K LI LGKERGYLT+ EIND LPED++D + +E I+  F  + I V E  +D
Sbjct: 1   MKDQQSRVKELIALGKERGYLTYGEINDHLPEDLVDADQVEDIVSMFSDLGIMVHEDGMD 60

Query: 96  TETL--MLSNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           T+ +  +   ++S+D+V +E   A L++ D +FGRT DP++MYMREMGSVELLTR+GEI 
Sbjct: 61  TDEMERLAEAVSSNDEVSDEEAAAVLASSDGEFGRTTDPVRMYMREMGSVELLTREGEIV 120

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE GL++ +  +S+ P  I   L   D +   E++++E++ G     F S   +++
Sbjct: 121 IAKRIEAGLRESLMMLSTYPACISSFLELYDAVEAGEMRLNELIKG-----FVSAEELVE 175

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKY---------------ESLIKFSNISFHFDKM 257
            + + ++         +D  ++  +                   E+ ++F  +   F+  
Sbjct: 176 EHDDLSDTDDDDADDDSDSDSDDDDDDSVDNVSDDDDSGEIDPEEARVRFEALKESFNAY 235

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
            KA   EG  +E+   +    S + +  + T K++  L D +   +N++   E+ I++IV
Sbjct: 236 LKA---EGEEAEA---SREQASAQFMEFKLTPKTLAYLNDLMSETVNEIRNQERIIMDIV 289

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V +  M R  FI  F  NE N+NW D   + +  Y+  + ++   I   Q  L  +    
Sbjct: 290 VEQARMNRRDFIDSFQGNESNVNWADKHIRAKKHYSSTIKKHHDEIIAAQSVLAEIAESR 349

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            + ++++++I+R+M   E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 350 GMSISEIKEISRQMSIAEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 409

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEY+RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R++RQ+L
Sbjct: 410 LMKAVDKFEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVARQML 469

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +++MPE+K+RK++KI+KEP+SME+P+GDDEDSHLGDF+ED N+++P
Sbjct: 470 QEMGREPTPDELAERVDMPEDKVRKVLKISKEPISMETPIGDDEDSHLGDFVEDVNVISP 529

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
           SD+A+   +R   + +LN LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 530 SDSAIIEGLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 589

Query: 618 AKALRKLR-PLAHDWL 632
           AKALRKLR P   D L
Sbjct: 590 AKALRKLRHPSRSDQL 605


>gi|422021797|ref|ZP_16368307.1| RNA polymerase sigma factor RpoD [Providencia sneebia DSM 19967]
 gi|414098394|gb|EKT60043.1| RNA polymerase sigma factor RpoD [Providencia sneebia DSM 19967]
          Length = 617

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/617 (50%), Positives = 418/617 (67%), Gaps = 18/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILAETSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 997
            KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 998  ------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
                     +  + +  +E    + S +D       +L  E   KFS +   ++K R+  
Sbjct: 183  IGSELPQEELDKDDDEEDEDEDGDDSDSDDDNSIDPELARE---KFSELREQYEKTRQHI 239

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            ++ G ++   + A   +S      R   K  + L + +R  +++V   E+ I++  V +C
Sbjct: 240  KQFGRSNAQTVLAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQERTIMKFCVEQC 299

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +
Sbjct: 300  KMPKKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTI 359

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 360  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 419

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 420  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 479

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 480  REPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 539

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 540  TSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 599

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 600  RKLRHPSRSEVLRSFLD 616



 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/604 (50%), Positives = 409/604 (67%), Gaps = 18/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILAETSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------- 207
           KRIE+G+  +  +++  P  I  +L   DK+   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDKVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 208 ------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
                    +  + +  +E    + S +D       +L  E   KFS +   ++K R+  
Sbjct: 183 IGSELPQEELDKDDDEEDEDEDGDDSDSDDDNSIDPELARE---KFSELREQYEKTRQHI 239

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           ++ G ++   + A   +S      R   K  + L + +R  +++V   E+ I++  V +C
Sbjct: 240 KQFGRSNAQTVLAIEELSEVFKQFRLVPKQFDYLVNNMREMMDRVRLQERTIMKFCVEQC 299

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +FI +F  NE +  W+     +   ++  L      I    Q+L  ++ +  L +
Sbjct: 300 KMPKKNFITLFSGNETSETWLTAAKAMNKPWSEKLLEVEEEILRCLQRLRQIEEETGLTI 359

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 360 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 419

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 420 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 479

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 480 REPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 539

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 540 TSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 599

Query: 622 RKLR 625
           RKLR
Sbjct: 600 RKLR 603


>gi|336451150|ref|ZP_08621595.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
            sigma factor, sigma-70 family [Idiomarina sp. A28L]
 gi|336281995|gb|EGN75241.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
            sigma factor, sigma-70 family [Idiomarina sp. A28L]
          Length = 610

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 311/602 (51%), Positives = 407/602 (67%), Gaps = 6/602 (0%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D + LM+S
Sbjct: 8    LKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFETAPDADDLMMS 67

Query: 893  NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 952
               +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+ 
Sbjct: 68   EDAADEDAAEEAAAALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGIN 127

Query: 953  DMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKI 1012
             +  +++  P  I  +L   D     +I++ EI+ G ID N      V   +  +     
Sbjct: 128  QVQCSVAEYPEAINFLLEQWDAYEAEQIRLTEIISGFIDPNEVEEAPVSATHIGSELSDD 187

Query: 1013 LIESSSADLSTEQLEKLKY------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
             +E    D   E  E+         E+  KF+ +   ++  R A +  G   +       
Sbjct: 188  QLEDGDDDDDDEDEEESTDTGVDPEEAREKFTELRAQYEATRDAIKTYGRGDDKTTAEIE 247

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +S      R   K  ++L   +R  +++V   E+ I+++ + +  +P+  F++ F  NE
Sbjct: 248  KLSELFKHFRLVPKQFDRLVKDMREMMDRVRVQERLIMKLCLEQAKLPKRTFVQAFAGNE 307

Query: 1127 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 1186
             +++W D     +  Y   L  +   +     KL  +  +  L +  ++DINR+M  GE 
Sbjct: 308  TSMSWFDAVIAKEKKYAEALEEHRDEVTRCSGKLRAIAEETGLSIAKVKDINRRMSIGEA 367

Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 368  KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 427

Query: 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306
            ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MP
Sbjct: 428  ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQPEELAERMAMP 487

Query: 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 1366
            E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA + S+++ V+D+L  
Sbjct: 488  EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLDLPVDAATSESLQNAVRDVLGG 547

Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +LK F
Sbjct: 548  LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLKSF 607

Query: 1427 LE 1428
            L+
Sbjct: 608  LD 609



 Score =  567 bits (1461), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 303/589 (51%), Positives = 397/589 (67%), Gaps = 6/589 (1%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D + LM+S
Sbjct: 8   LKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFETAPDADDLMMS 67

Query: 103 NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLK 162
              +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+ 
Sbjct: 68  EDAADEDAAEEAAAALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGIN 127

Query: 163 DMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKI 222
            +  +++  P  I  +L   D     +I++ EI+ G ID N      V   +  +     
Sbjct: 128 QVQCSVAEYPEAINFLLEQWDAYEAEQIRLTEIISGFIDPNEVEEAPVSATHIGSELSDD 187

Query: 223 LIESSSADLSTEQLEKLKY------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
            +E    D   E  E+         E+  KF+ +   ++  R A +  G   +       
Sbjct: 188 QLEDGDDDDDDEDEEESTDTGVDPEEAREKFTELRAQYEATRDAIKTYGRGDDKTTAEIE 247

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +S      R   K  ++L   +R  +++V   E+ I+++ + +  +P+  F++ F  NE
Sbjct: 248 KLSELFKHFRLVPKQFDRLVKDMREMMDRVRVQERLIMKLCLEQAKLPKRTFVQAFAGNE 307

Query: 337 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 396
            +++W D     +  Y   L  +   +     KL  +  +  L +  ++DINR+M  GE 
Sbjct: 308 TSMSWFDAVIAKEKKYAEALEEHRDEVTRCSGKLRAIAEETGLSIAKVKDINRRMSIGEA 367

Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
           KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 368 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 427

Query: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 516
           ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MP
Sbjct: 428 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPQPEELAERMAMP 487

Query: 517 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 576
           E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA + S+++ V+D+L  
Sbjct: 488 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLDLPVDAATSESLQNAVRDVLGG 547

Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 596


>gi|386286955|ref|ZP_10064135.1| transcription initiation factor sigma 70 [gamma proteobacterium
            BDW918]
 gi|385279994|gb|EIF43926.1| transcription initiation factor sigma 70 [gamma proteobacterium
            BDW918]
          Length = 604

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/606 (51%), Positives = 419/606 (69%), Gaps = 20/606 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V EH  D +TL++
Sbjct: 9    RLKQLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEEIIQMINDMGIQVFEHAPDEDTLIM 68

Query: 892  SNITSDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   S DD+  A  AA    V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG
Sbjct: 69   AGGDSPDDIAAAEAAAALAAVETETGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEG 128

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            +++++ A++  P  +  IL   DK++  E ++ +I+ G +  N + N +  +       E
Sbjct: 129  IREVMAALAYYPGVVTGILAQYDKVATEERRLGDIMSGYL--NPAENVQSPQQQAAAAAE 186

Query: 1011 KILIESSSADLSTEQLEKLKY----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
                 +++AD   E  E +      E+ I+F+ +    D++  +  + G  S+   K  N
Sbjct: 187  AAEANNTTADAEDED-EAVSGPDPEEARIRFAALQEQSDRVEASIAEHGRYSKQTAKELN 245

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +       + T    + L + +R  ++ +  +E++I+ + V   G+ R  FI+ F  NE
Sbjct: 246  ELGEIFKYFKLTPAMFDPLIEEVRTTLSSIRSMEREIMTVCVKNVGIDRKEFIRSFQGNE 305

Query: 1127 INLNWVDNETKIQH----DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
             NL W D   K +H    DY+ +       I+ LQ K+ +++    L ++D+++INR++ 
Sbjct: 306  ANLKWGDELLK-KHPKLADYSDV-------IRRLQNKIAHIEERQDLTISDIKEINRRVS 357

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 358  IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 417

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 418  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 477

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A    +R   KD
Sbjct: 478  MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPIESATGEGLREATKD 537

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 538  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDH 597

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 598  LRSFLD 603



 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/601 (51%), Positives = 413/601 (68%), Gaps = 21/601 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V EH  D +TL++
Sbjct: 9   RLKQLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEEIIQMINDMGIQVFEHAPDEDTLIM 68

Query: 102 SNITSDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   S DD+  A  AA    V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG
Sbjct: 69  AGGDSPDDIAAAEAAAALAAVETETGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEG 128

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           +++++ A++  P  +  IL   DK++  E ++ +I+ G +  N + N +  +       E
Sbjct: 129 IREVMAALAYYPGVVTGILAQYDKVATEERRLGDIMSGYL--NPAENVQSPQQQAAAAAE 186

Query: 221 KILIESSSADLSTEQLEKLKY----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
                +++AD   E  E +      E+ I+F+ +    D++  +  + G  S+   K  N
Sbjct: 187 AAEANNTTADAEDED-EAVSGPDPEEARIRFAALQEQSDRVEASIAEHGRYSKQTAKELN 245

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +       + T    + L + +R  ++ +  +E++I+ + V   G+ R  FI+ F  NE
Sbjct: 246 ELGEIFKYFKLTPAMFDPLIEEVRTTLSSIRSMEREIMTVCVKNVGIDRKEFIRSFQGNE 305

Query: 337 INLNWVDNETKIQH----DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
            NL W D   K +H    DY+ +       I+ LQ K+ +++    L ++D+++INR++ 
Sbjct: 306 ANLKWGDELLK-KHPKLADYSDV-------IRRLQNKIAHIEERQDLTISDIKEINRRVS 357

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 358 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 417

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +
Sbjct: 418 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGER 477

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A    +R   KD
Sbjct: 478 MEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTISSPIESATGEGLREATKD 537

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDW 631
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D 
Sbjct: 538 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDH 597

Query: 632 L 632
           L
Sbjct: 598 L 598


>gi|145597737|ref|YP_001161813.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
 gi|145209433|gb|ABP38840.1| RNA polymerase sigma factor RpoD [Yersinia pestis Pestoides F]
          Length = 608

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 418/612 (68%), Gaps = 17/612 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              +      ++    D   E    +  E +  KFS++   ++  R   +K G N      
Sbjct: 183  VGSELSTEEMDDEDEDDDAEDDNSIDPELARQKFSDLREQYENARMEIKKNGRN------ 236

Query: 1064 AHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C MP+ 
Sbjct: 237  -HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKK 295

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 296  NFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKD 355

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 356  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 415

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 416  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 475

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 476  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLKLPLDSATSESL 535

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 536  RSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 595

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 596  PSRSEVLRSFLD 607



 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/599 (50%), Positives = 409/599 (68%), Gaps = 17/599 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
             +      ++    D   E    +  E +  KFS++   ++  R   +K G N      
Sbjct: 183 VGSELSTEEMDDEDEDDDAEDDNSIDPELARQKFSDLREQYENARMEIKKNGRN------ 236

Query: 274 AHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C MP+ 
Sbjct: 237 -HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQCKMPKK 295

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++D
Sbjct: 296 NFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQKLRQIEEETGLTIEQVKD 355

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 356 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 415

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 416 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 475

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 476 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLKLPLDSATSESL 535

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 536 RSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|417428598|ref|ZP_12160913.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Mississippi str. A4-633]
 gi|353615874|gb|EHC67278.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica
            serovar Mississippi str. A4-633]
          Length = 673

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 313/668 (46%), Positives = 431/668 (64%), Gaps = 31/668 (4%)

Query: 792  DKYDPDSYIR----KFGYKIFSKKNAFSFDI----KSNSREEIENLRKKFKILIKLGKER 843
            D+  PDS       K+ Y +    ++++ D     K   R   +N + + K+L+  GKE+
Sbjct: 5    DREAPDSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQ 64

Query: 844  GYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVE 901
            GYLT++E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D E
Sbjct: 65   GYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAE 124

Query: 902  EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSC 961
            EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  
Sbjct: 125  EAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEY 184

Query: 962  PTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADL 1021
            P  I  +L   D++   E ++ +++ G +D N          +  +   +  ++    + 
Sbjct: 185  PEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDED 244

Query: 1022 STEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
              +  +    +        +  KF+ +   +   R   + +G +  +  +    +S    
Sbjct: 245  EEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFK 304

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +
Sbjct: 305  QFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFN 364

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                +   ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+
Sbjct: 365  AAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKK 424

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 425  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 484

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK+
Sbjct: 485  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKV 544

Query: 1314 MKIAKEPVSME-------------SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
            +KIAKEP+SME             SP+GDDEDSHLGDFIED  +  P D+A   S+R+  
Sbjct: 545  LKIAKEPISMETPIGKSQSPWKRRSPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAAT 604

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 605  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 664

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 665  EVLRSFLD 672



 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/650 (46%), Positives = 421/650 (64%), Gaps = 29/650 (4%)

Query: 5   NKKTKIKNKKTKETLLKNAFSFDIKSNSREEI------ENLRKKFKILIKLGKERGYLTF 58
           + +++ +  K K  L  N  S+ + +N   +       +N + + K+L+  GKE+GYLT+
Sbjct: 10  DSRSERQRPKYKYALALNVDSYTVDTNQTNKCGYRLMEQNPQSQLKLLVTRGKEQGYLTY 69

Query: 59  SEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITS-DDDVEEATEA 116
           +E+ND LPEDI+D + IE II+    M I V E   D + L+L+ N TS D+D EEA   
Sbjct: 70  AEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEEAAAQ 129

Query: 117 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIM 176
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P  I 
Sbjct: 130 VLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAIT 189

Query: 177 EILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQL 236
            +L   D++   E ++ +++ G +D N          +  +   +  ++    +   +  
Sbjct: 190 YLLEQYDRVEAEEARLSDLITGFVDPNAEEEMAPTATHVGSELSQEDLDDDEDEDEEDGD 249

Query: 237 EKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFT 288
           +    +        +  KF+ +   +   R   + +G +  +  +    +S      R  
Sbjct: 250 DDAADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLV 309

Query: 289 AKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348
            K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  NE +  W +    +
Sbjct: 310 PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSETWFNAAIAM 369

Query: 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEA 408
              ++  L      ++   QKL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EA
Sbjct: 370 NKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA 429

Query: 409 NLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468
           NLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
Sbjct: 430 NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 489

Query: 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK 528
           IADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAK
Sbjct: 490 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK 549

Query: 529 EPVSME-------------SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           EP+SME             SP+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L 
Sbjct: 550 EPISMETPIGKSQSPWKRRSPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 609

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 610 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 659


>gi|322831339|ref|YP_004211366.1| RNA polymerase sigma-70 subunit RpoD [Rahnella sp. Y9602]
 gi|383188571|ref|YP_005198699.1| sigma-70 family RNA polymerase sigma factor [Rahnella aquatilis CIP
            78.65 = ATCC 33071]
 gi|384256453|ref|YP_005400387.1| RNA polymerase sigma factor RpoD [Rahnella aquatilis HX2]
 gi|321166540|gb|ADW72239.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
 gi|371586829|gb|AEX50559.1| RNA polymerase sigma factor, sigma-70 family [Rahnella aquatilis CIP
            78.65 = ATCC 33071]
 gi|380752429|gb|AFE56820.1| RNA polymerase sigma factor RpoD [Rahnella aquatilis HX2]
          Length = 612

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 418/611 (68%), Gaps = 11/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+    D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENRPDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N  +   +    
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEVRLSDLITGFVDPN--AEEEIAPTA 180

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
             +   E    E    D   ++ +  + ++ I       KF+ +    +  R   +K G +
Sbjct: 181  THVGSELTTEEQDDDDEDEDEDDDAEDDNSIDPELARQKFTELREQHEATRLVIKKNGRS 240

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +S  +    +S+     R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 241  HKSAAEEILKLSDVFKQFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKVCVEQCKMPKKN 300

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+ +F  NE +  W D    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 301  FVNLFAGNETSDTWFDAALAMGKPWSEKLKEVTEDVQRGLMKLRQIEEETGLTIEQVKDI 360

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 361  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 420

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 421  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 480

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 481  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 540

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 541  SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 600

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 601  SRSEVLRSFLD 611



 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 409/598 (68%), Gaps = 11/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+    D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENRPDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N  +   +    
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEVRLSDLITGFVDPN--AEEEIAPTA 180

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
            +   E    E    D   ++ +  + ++ I       KF+ +    +  R   +K G +
Sbjct: 181 THVGSELTTEEQDDDDEDEDEDDDAEDDNSIDPELARQKFTELREQHEATRLVIKKNGRS 240

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +S  +    +S+     R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 241 HKSAAEEILKLSDVFKQFRLVPKQFDFLVNSMRSMMDRVRAQERLIMKVCVEQCKMPKKN 300

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+ +F  NE +  W D    +   ++  L      ++    KL  ++ +  L +  ++DI
Sbjct: 301 FVNLFAGNETSDTWFDAALAMGKPWSEKLKEVTEDVQRGLMKLRQIEEETGLTIEQVKDI 360

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 361 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 420

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 421 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 480

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 481 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 540

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|253686949|ref|YP_003016139.1| RNA polymerase sigma-70 subunit RpoD [Pectobacterium carotovorum
            subsp. carotovorum PC1]
 gi|251753527|gb|ACT11603.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium carotovorum
            subsp. carotovorum PC1]
          Length = 612

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/611 (50%), Positives = 419/611 (68%), Gaps = 11/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +  +    
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEED--IAPTA 180

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
             +   E    E    D  +E  +  + ++ I       KF+ +   ++  RK  ++ G +
Sbjct: 181  THVGSELSSEEMDDDDEESEDDDDSEDDNSIDPELAREKFTELRDQYETTRKVIKEHGRS 240

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                ++   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 241  HALAVQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKN 300

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 301  FVTMFTGNETNSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDI 360

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 361  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 420

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 421  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 480

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 481  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 540

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 541  SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 600

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 601  SRSEVLRSFLD 611



 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/598 (50%), Positives = 410/598 (68%), Gaps = 11/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +  +    
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEED--IAPTA 180

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
            +   E    E    D  +E  +  + ++ I       KF+ +   ++  RK  ++ G +
Sbjct: 181 THVGSELSSEEMDDDDEESEDDDDSEDDNSIDPELAREKFTELRDQYETTRKVIKEHGRS 240

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
               ++   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 241 HALAVQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKN 300

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 301 FVTMFTGNETNSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDI 360

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 361 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 420

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 421 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 480

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 481 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 540

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|238756616|ref|ZP_04617911.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
 gi|238705164|gb|EEP97586.1| RNA polymerase sigma factor rpoD [Yersinia ruckeri ATCC 29473]
          Length = 613

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 312/624 (50%), Positives = 418/624 (66%), Gaps = 36/624 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTNDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIIGFVDPN----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI------------------KFSNISFHF 1044
                EE I   ++   ++LST ++   + E                     KFS++   +
Sbjct: 172  ---AEEDIAPTATHVGSELSTAEMGDDENEDEDEDDDSEDDNSIDPELARQKFSDLREQY 228

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +  RK  +K G +  S       +S      R   K  + L + +R  +++V   E+ I+
Sbjct: 229  ENARKEIKKNGRSHISAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRVRTQERIIM 288

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            ++ V +C MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++
Sbjct: 289  KLCVEQCKMPKKNFVTLFASNETSDTWFAAALAMGKPWSEKLKDVSDDVQRSLQKLRQIE 348

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349  EETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469  QMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL 528

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
              P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529  ELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  QIEAKALRKLRHPSRSEVLRSFLD 612



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 305/611 (49%), Positives = 409/611 (66%), Gaps = 36/611 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTNDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLIIGFVDPN----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI------------------KFSNISFHF 254
               EE I   ++   ++LST ++   + E                     KFS++   +
Sbjct: 172 ---AEEDIAPTATHVGSELSTAEMGDDENEDEDEDDDSEDDNSIDPELARQKFSDLREQY 228

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +  RK  +K G +  S       +S      R   K  + L + +R  +++V   E+ I+
Sbjct: 229 ENARKEIKKNGRSHISAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRVRTQERIIM 288

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           ++ V +C MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++
Sbjct: 289 KLCVEQCKMPKKNFVTLFASNETSDTWFAAALAMGKPWSEKLKDVSDDVQRSLQKLRQIE 348

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349 EETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469 QMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL 528

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
             P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529 ELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 589 QIEAKALRKLR 599


>gi|152984199|ref|YP_001346113.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PA7]
 gi|150959357|gb|ABR81382.1| sigma factor RpoD [Pseudomonas aeruginosa PA7]
          Length = 617

 Score =  583 bits (1504), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 313/607 (51%), Positives = 420/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130  REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 1010 EKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                 +    + S +  +            E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190  ADSKEKDDEEEESDDNSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
                  ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250  TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310  FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490  RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/594 (51%), Positives = 411/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130 REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 220 EKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                +    + S +  +            E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190 ADSKEKDDEEEESDDNSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
                 ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250 TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310 FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490 RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|227113748|ref|ZP_03827404.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
            brasiliensis PBR1692]
          Length = 611

 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/619 (50%), Positives = 416/619 (67%), Gaps = 28/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 993
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 SS        +  +EE+    S   +L+ E           KF+ +   ++  R+
Sbjct: 183  VGSELSSEEMDDDDEEEEDEEEEDDNSIDPELARE-----------KFTELREQYETTRQ 231

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              +  G +     +   N+S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 232  VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVE 291

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +C MP+ +F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292  QCKMPKKNFVTMFTGNETNSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGL 351

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532  SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 592  ALRKLRHPSRSEVLRSFLD 610



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/606 (50%), Positives = 407/606 (67%), Gaps = 28/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 203
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                SS        +  +EE+    S   +L+ E           KF+ +   ++  R+
Sbjct: 183 VGSELSSEEMDDDDEEEEDEEEEDDNSIDPELARE-----------KFTELREQYETTRQ 231

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             +  G +     +   N+S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 232 VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVE 291

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +C MP+ +F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292 QCKMPKKNFVTMFTGNETNSTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGL 351

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532 SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 592 ALRKLR 597


>gi|85711761|ref|ZP_01042817.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
            OS145]
 gi|85694376|gb|EAQ32318.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina baltica
            OS145]
          Length = 611

 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 312/609 (51%), Positives = 414/609 (67%), Gaps = 8/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+G+LTF+E+ND LP++I+D + IE II+    M I V E   D 
Sbjct: 3    QNRQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIRVFESAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM+S   +D+D  E    AL+TVD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMMSESAADEDAAEEAAQALATVDGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D     E+++ EI+ G ID +   +   +     
Sbjct: 123  IEDGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTEIIVGFIDPD-EVDEAPVSATHV 181

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 1059
             +E          D   +  ++ + +S I       KF+ +   ++  R+A  + G    
Sbjct: 182  GSELSEDELEDEDDDDEDDDDEEENDSGIDPEFARQKFTELREQYEATRQAITQFGREHP 241

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
                  + +S+     R   K  ++L   +R  + +V   E+ +++  V + GMP+  F+
Sbjct: 242  DARVEIDKLSDLFKQFRLVPKQFDRLVQDMRAMMQRVRVQERLVMKAAVEQAGMPKRAFM 301

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            K F  NE +L WVD +     DY   L      I+    KL  ++ +  L +  ++DINR
Sbjct: 302  KAFAGNENSLAWVDEQISAGVDYATTLQEARVEIERCVTKLNEIEKETGLTIAKVKDINR 361

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 362  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 421

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 422  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEEL 481

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R+ 
Sbjct: 482  AERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNS 541

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            V+D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 542  VRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 601

Query: 1420 YYKLKIFLE 1428
              +LK FL+
Sbjct: 602  SEQLKSFLD 610



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/596 (51%), Positives = 404/596 (67%), Gaps = 8/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+G+LTF+E+ND LP++I+D + IE II+    M I V E   D 
Sbjct: 3   QNRQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQIEDIIRMINDMGIRVFESAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM+S   +D+D  E    AL+TVD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMMSESAADEDAAEEAAQALATVDGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D     E+++ EI+ G ID +   +   +     
Sbjct: 123 IEDGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTEIIVGFIDPD-EVDEAPVSATHV 181

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSE 269
            +E          D   +  ++ + +S I       KF+ +   ++  R+A  + G    
Sbjct: 182 GSELSEDELEDEDDDDEDDDDEEENDSGIDPEFARQKFTELREQYEATRQAITQFGREHP 241

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
                 + +S+     R   K  ++L   +R  + +V   E+ +++  V + GMP+  F+
Sbjct: 242 DARVEIDKLSDLFKQFRLVPKQFDRLVQDMRAMMQRVRVQERLVMKAAVEQAGMPKRAFM 301

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           K F  NE +L WVD +     DY   L      I+    KL  ++ +  L +  ++DINR
Sbjct: 302 KAFAGNENSLAWVDEQISAGVDYATTLQEARVEIERCVTKLNEIEKETGLTIAKVKDINR 361

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 362 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 421

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 422 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEEL 481

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R+ 
Sbjct: 482 AERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNS 541

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           V+D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 542 VRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|329298675|ref|ZP_08256011.1| RNA polymerase sigma factor RpoD [Plautia stali symbiont]
          Length = 610

 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/620 (50%), Positives = 417/620 (67%), Gaps = 31/620 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GK +GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKVQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +  +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   N   +   
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEN---LAPT 179

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +   ++  E    D   ++       S+       KF+++   ++  R   + +G + 
Sbjct: 180  ATHVGSELSEEDRDDDEEEDEESDDDDNSIDPELAREKFNDLRTQYETTRTVIKAKGRSH 239

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               +   NN+S      R   K  + L + +R  + +V   E+ I+++ V  C MP+ +F
Sbjct: 240  ADAVAEINNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCVELCKMPKKNF 299

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDIV 1168
            I +F  NE + +W          +   L  N P  ++LQ          QKL+ ++ +  
Sbjct: 300  ITLFTGNETSESW----------FKTALAMNKPWSEKLQEVEKDVMRSLQKLLQIEEETG 349

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 350  LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 409

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 410  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 469

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P 
Sbjct: 470  EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL 529

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 530  DSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 589

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   L+ FL+
Sbjct: 590  KALRKLRHPSRSEVLRSFLD 609



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/607 (49%), Positives = 408/607 (67%), Gaps = 31/607 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GK +GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKVQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +  +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   N   +   
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEN---LAPT 179

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +   ++  E    D   ++       S+       KF+++   ++  R   + +G + 
Sbjct: 180 ATHVGSELSEEDRDDDEEEDEESDDDDNSIDPELAREKFNDLRTQYETTRTVIKAKGRSH 239

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              +   NN+S      R   K  + L + +R  + +V   E+ I+++ V  C MP+ +F
Sbjct: 240 ADAVAEINNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCVELCKMPKKNF 299

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDIV 378
           I +F  NE + +W          +   L  N P  ++LQ          QKL+ ++ +  
Sbjct: 300 ITLFTGNETSESW----------FKTALAMNKPWSEKLQEVEKDVMRSLQKLLQIEEETG 349

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 350 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 409

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 410 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 469

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P 
Sbjct: 470 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL 529

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 530 DSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 589

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 590 KALRKLR 596


>gi|238794325|ref|ZP_04637937.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
 gi|238726319|gb|EEQ17861.1| RNA polymerase sigma factor rpoD [Yersinia intermedia ATCC 29909]
          Length = 612

 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 313/630 (49%), Positives = 423/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ ++++G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 1045
                EE I   ++   ++LST +++    E                    KFS++   ++
Sbjct: 172  ---AEEDIAPTATHVGSELSTAEMDDDDDEDEDEDEEEDDNSIDPELARQKFSDLREQYE 228

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 1098
              R   +K G       ++H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229  NARMEIKKNG-------RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRVRT 281

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
             E+ I+++ V +C MP+ +F+ +F  NE +  W      +   ++  L      ++   Q
Sbjct: 282  QERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQ 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462  LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/617 (49%), Positives = 414/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ ++++G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLINGFVDPN----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 255
               EE I   ++   ++LST +++    E                    KFS++   ++
Sbjct: 172 ---AEEDIAPTATHVGSELSTAEMDDDDDEDEDEDEEEDDNSIDPELARQKFSDLREQYE 228

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 308
             R   +K G       ++H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229 NARMEIKKNG-------RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRTMMDRVRT 281

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
            E+ I+++ V +C MP+ +F+ +F  NE +  W      +   ++  L      ++   Q
Sbjct: 282 QERIIMKLCVEQCKMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQ 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|1072030|gb|AAB60181.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 603

 Score =  583 bits (1503), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/603 (50%), Positives = 414/603 (68%), Gaps = 4/603 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S  GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESQIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NN-EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
            +   ++ L +  SAD       +L  E   KF+ +   +   R   + +G +  +  +  
Sbjct: 183  SELSQEDLGDDDSADDDNSIDPELARE---KFAELRAQYVVTRDTIKAKGRSHATAQEEI 239

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  N
Sbjct: 240  LKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGN 299

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E +  W +    +   ++  L      +    QKL  ++ +  L +  ++DINR+M  GE
Sbjct: 300  ETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGE 359

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 360  AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 419

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M M
Sbjct: 420  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 479

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L 
Sbjct: 480  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 539

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ 
Sbjct: 540  GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 599

Query: 1426 FLE 1428
            FL+
Sbjct: 600  FLD 602



 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/590 (50%), Positives = 405/590 (68%), Gaps = 4/590 (0%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S  GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESQIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NN-EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
           +   ++ L +  SAD       +L  E   KF+ +   +   R   + +G +  +  +  
Sbjct: 183 SELSQEDLGDDDSADDDNSIDPELARE---KFAELRAQYVVTRDTIKAKGRSHATAQEEI 239

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI +F  N
Sbjct: 240 LKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGN 299

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E +  W +    +   ++  L      +    QKL  ++ +  L +  ++DINR+M  GE
Sbjct: 300 ETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGE 359

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 360 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 419

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M M
Sbjct: 420 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 479

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   D+L 
Sbjct: 480 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLA 539

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 540 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 589


>gi|336233141|ref|YP_004589887.1| RNA polymerase sigma-70 factor [Buchnera aphidicola (Cinara
            tujafilina)]
 gi|335345082|gb|AEH39628.1| RNA polymerase sigma-70 factor [Buchnera aphidicola (Cinara
            tujafilina)]
          Length = 614

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 314/620 (50%), Positives = 420/620 (67%), Gaps = 38/620 (6%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + KIL+  GKE+GYLT++EI+D LP+DII+ + I++II+  +   I V E   D   L+L
Sbjct: 8    QLKILVSHGKEQGYLTYAEIHDHLPDDIINSDQIKNIIQMIKDFGIQVVEEARDAGNLIL 67

Query: 892  SNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            +   +D D E+A E A   LS V+++ GRT DPI+MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 68   NETPTDTD-EDAVEVAAQVLSHVETELGRTTDPIRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----------N 997
            EG+  +  + S  P  I  +L    K+   +IK+ EI+ G +D N  +           N
Sbjct: 127  EGVNQVQSSFSEYPQAIAYLLEQYHKVESGDIKLSEIISGFVDPNIENTLFPITTIDVLN 186

Query: 998  NRVIKGN---------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
            N  IK            N+ +E+ LI+ + A     QL+   Y        I+ +  K +
Sbjct: 187  NSTIKKEIKTLNINPVSNDQDEENLIDPNIAKEKFLQLQTQYY--------ITNYIIKTK 238

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
                K        I A   +S      R   K  + L + +RN ++++ +  K+ILE+ V
Sbjct: 239  NRTHKNA------ITAIKELSEIFKQFRLAPKQFDYLVNNIRNILSKIQKKRKKILEVCV 292

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            + C MP+ +FI+ F   E +  W      +   +++ LC     I ++ ++L+ ++  I 
Sbjct: 293  DICKMPKKNFIQFFKGQETSQKWFYAAINMNAPWSIKLCEFQNDIFKILRELLIIEKKIG 352

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +   +DIN++M +GE+KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 353  LTIEQAKDINKRMSSGEIKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR +LQ
Sbjct: 413  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRYMLQ 472

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED N+  P 
Sbjct: 473  EIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTNLELPL 532

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            ++A + S+R++  D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 533  ESATSESLRTITHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 592

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   LK FL+
Sbjct: 593  KALRKLRHPSRSEILKSFLD 612



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/607 (50%), Positives = 411/607 (67%), Gaps = 38/607 (6%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + KIL+  GKE+GYLT++EI+D LP+DII+ + I++II+  +   I V E   D   L+L
Sbjct: 8   QLKILVSHGKEQGYLTYAEIHDHLPDDIINSDQIKNIIQMIKDFGIQVVEEARDAGNLIL 67

Query: 102 SNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           +   +D D E+A E A   LS V+++ GRT DPI+MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 68  NETPTDTD-EDAVEVAAQVLSHVETELGRTTDPIRMYMREMGTVELLTREGEIDIAKRIE 126

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----------N 207
           EG+  +  + S  P  I  +L    K+   +IK+ EI+ G +D N  +           N
Sbjct: 127 EGVNQVQSSFSEYPQAIAYLLEQYHKVESGDIKLSEIISGFVDPNIENTLFPITTIDVLN 186

Query: 208 NRVIKGN---------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
           N  IK            N+ +E+ LI+ + A     QL+   Y        I+ +  K +
Sbjct: 187 NSTIKKEIKTLNINPVSNDQDEENLIDPNIAKEKFLQLQTQYY--------ITNYIIKTK 238

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
               K        I A   +S      R   K  + L + +RN ++++ +  K+ILE+ V
Sbjct: 239 NRTHKNA------ITAIKELSEIFKQFRLAPKQFDYLVNNIRNILSKIQKKRKKILEVCV 292

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           + C MP+ +FI+ F   E +  W      +   +++ LC     I ++ ++L+ ++  I 
Sbjct: 293 DICKMPKKNFIQFFKGQETSQKWFYAAINMNAPWSIKLCEFQNDIFKILRELLIIEKKIG 352

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +   +DIN++M +GE+KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 353 LTIEQAKDINKRMSSGEIKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR +LQ
Sbjct: 413 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRYMLQ 472

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP P  ++ KM +PE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED N+  P 
Sbjct: 473 EIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTNLELPL 532

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           ++A + S+R++  D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 533 ESATSESLRTITHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 592

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 593 KALRKLR 599


>gi|50119628|ref|YP_048795.1| RNA polymerase sigma factor RpoD [Pectobacterium atrosepticum
            SCRI1043]
 gi|49610154|emb|CAG73594.1| RNA polymerase sigma-70 factor [Pectobacterium atrosepticum SCRI1043]
          Length = 611

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/619 (50%), Positives = 416/619 (67%), Gaps = 28/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 993
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 SS        + + +E+    S   +L+ E           KF+ +   ++  RK
Sbjct: 183  VGSELSSEEISDNDEEEDEDEEEDDNSIDPELARE-----------KFTELREQYETTRK 231

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              +  G +     +   N+S      R   K  + L +++R  +++V   E+ I+++ V 
Sbjct: 232  VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERLIIKLCVE 291

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +C MP+ +F+ +F  NE N +W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292  QCKMPKKNFVTMFTSNETNNSWFAAAVAMGKPWSEKLNDVAEDVTRSLQKLKQIEEETGL 351

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532  SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 592  ALRKLRHPSRSEVLRSFLD 610



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/606 (50%), Positives = 407/606 (67%), Gaps = 28/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 203
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                SS        + + +E+    S   +L+ E           KF+ +   ++  RK
Sbjct: 183 VGSELSSEEISDNDEEEDEDEEEDDNSIDPELARE-----------KFTELREQYETTRK 231

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             +  G +     +   N+S      R   K  + L +++R  +++V   E+ I+++ V 
Sbjct: 232 VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRTMMDRVRTQERLIIKLCVE 291

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +C MP+ +F+ +F  NE N +W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292 QCKMPKKNFVTMFTSNETNNSWFAAAVAMGKPWSEKLNDVAEDVTRSLQKLKQIEEETGL 351

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532 SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 592 ALRKLR 597


>gi|254480921|ref|ZP_05094167.1| Sigma-70, non-essential region family [marine gamma proteobacterium
            HTCC2148]
 gi|214038716|gb|EEB79377.1| Sigma-70, non-essential region family [marine gamma proteobacterium
            HTCC2148]
          Length = 605

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 420/608 (69%), Gaps = 10/608 (1%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            ++ N + + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    M I V E   
Sbjct: 3    DVVNQQSRLKALIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDMGIQVFEQAP 62

Query: 885  DTETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            D + L+++  + ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63   DADELLMTEGDRSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIV 122

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNFSSNNRV 1000
            IAKRIEEG+++++ A++  P  +  IL   + ++K E K+ +I+ G +D  ++  +   +
Sbjct: 123  IAKRIEEGIRELLSALALYPGAVKSILDEYELVTKEERKLADIMVGYLDPAQHVPTAAEL 182

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             +  +   ++    E    D   + +E  K     +F+ +   ++K  K   ++G    +
Sbjct: 183  AEAAQAKADKAGTDEEEETDNGPDPVEAKK-----RFTALKRQYNKTEKVIAEKGRTDAA 237

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             IK    +       + T +  + + DT RN +  V   E++I+ I +  CGMPR  FI 
Sbjct: 238  AIKEMEKLGELFKFFKLTPRVFDPISDTPRNILAAVRDQEREIMRIAIKVCGMPRKDFIS 297

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  +E +L W+  + + + DY   L      I  LQ+++  ++    L ++++++INR+
Sbjct: 298  TFQGSESDLKWLSRQAR-KKDYGPKLNAEKEIIHRLQRRIQAIEGQCGLQISEIKEINRR 356

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 357  MSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 416

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 417  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 476

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    ++   
Sbjct: 477  ERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTISSPVDSATGQGLQEAT 536

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            KD+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R 
Sbjct: 537  KDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 596

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 597  DYLRSFLD 604



 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 299/603 (49%), Positives = 415/603 (68%), Gaps = 11/603 (1%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           ++ N + + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    M I V E   
Sbjct: 3   DVVNQQSRLKALIAKGKEQGYLTYAEVNDHLPQDISDPDQVEDIIQMINDMGIQVFEQAP 62

Query: 95  DTETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           D + L+++  + ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63  DADELLMTEGDRSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIV 122

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNFSSNNRV 210
           IAKRIEEG+++++ A++  P  +  IL   + ++K E K+ +I+ G +D  ++  +   +
Sbjct: 123 IAKRIEEGIRELLSALALYPGAVKSILDEYELVTKEERKLADIMVGYLDPAQHVPTAAEL 182

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
            +  +   ++    E    D   + +E  K     +F+ +   ++K  K   ++G    +
Sbjct: 183 AEAAQAKADKAGTDEEEETDNGPDPVEAKK-----RFTALKRQYNKTEKVIAEKGRTDAA 237

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            IK    +       + T +  + + DT RN +  V   E++I+ I +  CGMPR  FI 
Sbjct: 238 AIKEMEKLGELFKFFKLTPRVFDPISDTPRNILAAVRDQEREIMRIAIKVCGMPRKDFIS 297

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  +E +L W+  + + + DY   L      I  LQ+++  ++    L ++++++INR+
Sbjct: 298 TFQGSESDLKWLSRQAR-KKDYGPKLNAEKEIIHRLQRRIQAIEGQCGLQISEIKEINRR 356

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 357 MSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 416

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 417 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 476

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    ++   
Sbjct: 477 ERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTISSPVDSATGQGLQEAT 536

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAH 629
           KD+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   
Sbjct: 537 KDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRS 596

Query: 630 DWL 632
           D+L
Sbjct: 597 DYL 599


>gi|403057012|ref|YP_006645229.1| sigma-70 factor (RpoD) [Pectobacterium carotovorum subsp. carotovorum
            PCC21]
 gi|402804338|gb|AFR01976.1| putative sigma-70 factor (RpoD) [Pectobacterium carotovorum subsp.
            carotovorum PCC21]
          Length = 611

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/619 (50%), Positives = 417/619 (67%), Gaps = 28/619 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 993
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 994  ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                 SS        + ++EE+    S   +L+ E           KF+ +   ++  R+
Sbjct: 183  VGSELSSEEMDDDDEEEDDEEEEDDNSIDPELARE-----------KFTELREQYETTRQ 231

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
              +  G +     +   N+S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 232  VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVE 291

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +C MP+ +F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292  QCKMPKKNFVTMFTGNETNNTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGL 351

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352  TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472  MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532  SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 592  ALRKLRHPSRSEVLRSFLD 610



 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/606 (50%), Positives = 408/606 (67%), Gaps = 28/606 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------- 203
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 204 ----FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                SS        + ++EE+    S   +L+ E           KF+ +   ++  R+
Sbjct: 183 VGSELSSEEMDDDDEEEDDEEEEDDNSIDPELARE-----------KFTELREQYETTRQ 231

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
             +  G +     +   N+S      R   K  + L +++R+ +++V   E+ I+++ V 
Sbjct: 232 VIKAHGRSHALAAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVE 291

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +C MP+ +F+ +F  NE N  W      +   ++  L      +    QKL  ++ +  L
Sbjct: 292 QCKMPKKNFVTMFTGNETNNTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGL 351

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 352 TIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 411

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 412 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 471

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D
Sbjct: 472 MGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLD 531

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 532 SATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 591

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 592 ALRKLR 597


>gi|398791798|ref|ZP_10552499.1| RNA polymerase sigma factor, sigma-70 family [Pantoea sp. YR343]
 gi|398214526|gb|EJN01102.1| RNA polymerase sigma factor, sigma-70 family [Pantoea sp. YR343]
          Length = 613

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 409/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G ID N   +      N
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGDARLSDLIIGFIDPNAEEDIAPTATN 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +   +   +    +   +        S+       KF ++   ++  R   + +G + 
Sbjct: 183  VGSELSQEDRDDDEEEDEDDDDSSDDDNSIDPELAREKFGDLRTQYETTRTVIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               +    N+S      R   K  + L + +R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243  ADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE N +W      +   ++  L      +     KL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETNPSWFKAALAMNKPWSEKLLEVEDDVNRSLYKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 296/597 (49%), Positives = 400/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G ID N   +      N
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGDARLSDLIIGFIDPNAEEDIAPTATN 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +   +   +    +   +        S+       KF ++   ++  R   + +G + 
Sbjct: 183 VGSELSQEDRDDDEEEDEDDDDSSDDDNSIDPELAREKFGDLRTQYETTRTVIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              +    N+S      R   K  + L + +R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243 ADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE N +W      +   ++  L      +     KL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETNPSWFKAALAMNKPWSEKLLEVEDDVNRSLYKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|389795244|ref|ZP_10198374.1| RNA polymerase sigma factor RpoD [Rhodanobacter fulvus Jip2]
 gi|388431021|gb|EIL88125.1| RNA polymerase sigma factor RpoD [Rhodanobacter fulvus Jip2]
          Length = 626

 Score =  583 bits (1502), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/613 (50%), Positives = 416/613 (67%), Gaps = 16/613 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM- 890
            + K LI  G E+GYLT++EIND LP+D++D E IE I+   + + I V +   DT+T+  
Sbjct: 12   EIKALISKGLEQGYLTYAEINDHLPDDVVDPEQIEDIMAVLKGVGIEVHDAAPDTDTIAD 71

Query: 891  ---LSNITSDDDVEEATEAAL-STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                 N + DD+       AL S VD++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 72   GAAPGNTSGDDEAAAEEAVALLSAVDAEVGRTTDPVRMYMREMGTVELLTREGEIAIAKR 131

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--------- 997
            IEEGL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++         
Sbjct: 132  IEEGLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAADLARKEKEAA 191

Query: 998  -NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EG 1055
               + + + N++ E    ++   +           E   +   +  ++ K +KA  K + 
Sbjct: 192  AALLPEPDPNDDSEGDDDDAEEEEEEAGPTGPDPEEVKRRMELLRDYYAKFQKAAPKADS 251

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               +  +K  + ++ E L ++  +  I+     LR  +  +   E+ +++I V +  MP+
Sbjct: 252  ILDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVGDIRHHERALMDIFVKQVKMPK 311

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              FIK FP NE NL W    ++ +  ++  +  +  +I   Q+KL  ++  + LPL D++
Sbjct: 312  TEFIKTFPSNEGNLEWAAELSRKRQKWSPNVKTHREAIDAEQEKLAAIERKLFLPLIDIK 371

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR M +GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 372  DINRAMASGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 431

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  
Sbjct: 432  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREAT 491

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D+A    
Sbjct: 492  PEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPIDSATETG 551

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552  LMETVRDVLGGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR  +L+ FL+
Sbjct: 612  HPSRSEQLRSFLD 624



 Score =  567 bits (1461), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 301/600 (50%), Positives = 406/600 (67%), Gaps = 16/600 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM- 100
           + K LI  G E+GYLT++EIND LP+D++D E IE I+   + + I V +   DT+T+  
Sbjct: 12  EIKALISKGLEQGYLTYAEINDHLPDDVVDPEQIEDIMAVLKGVGIEVHDAAPDTDTIAD 71

Query: 101 ---LSNITSDDDVEEATEAAL-STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                N + DD+       AL S VD++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 72  GAAPGNTSGDDEAAAEEAVALLSAVDAEVGRTTDPVRMYMREMGTVELLTREGEIAIAKR 131

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN--------- 207
           IEEGL  +  A++S P TI  +L   D+    + ++ EI+ G +D   +++         
Sbjct: 132 IEEGLGQVQTALASFPLTIELLLEEYDQHLDGKRRLSEILAGFLDLEEAADLARKEKEAA 191

Query: 208 -NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK-EG 265
              + + + N++ E    ++   +           E   +   +  ++ K +KA  K + 
Sbjct: 192 AALLPEPDPNDDSEGDDDDAEEEEEEAGPTGPDPEEVKRRMELLRDYYAKFQKAAPKADS 251

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              +  +K  + ++ E L ++  +  I+     LR  +  +   E+ +++I V +  MP+
Sbjct: 252 ILDKKIVKLRDQMAEEFLKLKLPSALIDGFVRKLREVVGDIRHHERALMDIFVKQVKMPK 311

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             FIK FP NE NL W    ++ +  ++  +  +  +I   Q+KL  ++  + LPL D++
Sbjct: 312 TEFIKTFPSNEGNLEWAAELSRKRQKWSPNVKTHREAIDAEQEKLAAIERKLFLPLIDIK 371

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR M +GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 372 DINRAMASGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 431

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  
Sbjct: 432 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREAT 491

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D+A    
Sbjct: 492 PEELAKEMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGNASSPIDSATETG 551

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 LMETVRDVLGGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611


>gi|410860340|ref|YP_006975574.1| RNA polymerase sigma factor [Alteromonas macleodii AltDE1]
 gi|410817602|gb|AFV84219.1| RNA polymerase sigma factor [Alteromonas macleodii AltDE1]
          Length = 611

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/603 (51%), Positives = 413/603 (68%), Gaps = 6/603 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8    QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
                +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68   QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVIKGNKNNN 1008
              +  +++  P  I  +L   D     EI++ +I+ G +D N   +        G++ + 
Sbjct: 128  NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDDQDLAPTATHVGSELSE 187

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
            EE    +    +   E+ +    +  +   +FS +   + K R+  EK+G +        
Sbjct: 188  EELDDEDGDDDEDEDEEEDDSGVDPELARERFSELREQYIKTREVIEKKGRSHADSRTQI 247

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
            N +S+     R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F  N
Sbjct: 248  NALSDVFKEFRLVPKQFDRMVKNMRAMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGN 307

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  GE
Sbjct: 308  ETSTAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSIGE 367

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 368  AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M M
Sbjct: 428  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLM 487

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L 
Sbjct: 488  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKGATQEVLA 547

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ 
Sbjct: 548  GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRS 607

Query: 1426 FLE 1428
            FL+
Sbjct: 608  FLD 610



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 302/590 (51%), Positives = 403/590 (68%), Gaps = 6/590 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8   QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
               +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68  QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVIKGNKNNN 218
             +  +++  P  I  +L   D     EI++ +I+ G +D N   +        G++ + 
Sbjct: 128 NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDDQDLAPTATHVGSELSE 187

Query: 219 EEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
           EE    +    +   E+ +    +  +   +FS +   + K R+  EK+G +        
Sbjct: 188 EELDDEDGDDDEDEDEEEDDSGVDPELARERFSELREQYIKTREVIEKKGRSHADSRTQI 247

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
           N +S+     R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F  N
Sbjct: 248 NALSDVFKEFRLVPKQFDRMVKNMRAMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGN 307

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  GE
Sbjct: 308 ETSTAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSIGE 367

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 368 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M M
Sbjct: 428 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLM 487

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L 
Sbjct: 488 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKGATQEVLA 547

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|352100252|ref|ZP_08958059.1| RNA polymerase sigma factor RpoD [Halomonas sp. HAL1]
 gi|350601277|gb|EHA17326.1| RNA polymerase sigma factor RpoD [Halomonas sp. HAL1]
          Length = 616

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 316/607 (52%), Positives = 404/607 (66%), Gaps = 11/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   SDQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130  REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 1062
            E  L E    +   E  +    E           F+++R+       AF K G  S    
Sbjct: 190  ESELEEDVEGEGDEEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKHGRGSAELK 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250  AEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 1181
            P NE    W+D+    Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310  PGNESRKTWLDDFQAAQSKYADRLEPLRADIARAQRK-IAFEEDMVQLSVADLKEVNRKL 368

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489  RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 549  NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 608

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 609  PLRSFLD 615



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 309/594 (52%), Positives = 395/594 (66%), Gaps = 11/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  SDQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130 REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 272
           E  L E    +   E  +    E           F+++R+       AF K G  S    
Sbjct: 190 ESELEEDVEGEGDEEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKHGRGSAELK 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250 AEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 391
           P NE    W+D+    Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310 PGNESRKTWLDDFQAAQSKYADRLEPLRADIARAQRK-IAFEEDMVQLSVADLKEVNRKL 368

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489 RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|37678745|ref|NP_933354.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
 gi|37197486|dbj|BAC93325.1| RNA polymerase sigma factor RpoD [Vibrio vulnificus YJ016]
          Length = 643

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 318/637 (49%), Positives = 423/637 (66%), Gaps = 53/637 (8%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D +
Sbjct: 23   NPQSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 82

Query: 888  TLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             L LS+ T  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 83   DLALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 142

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          + 
Sbjct: 143  RIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNADETAAPTATH- 201

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYE------------------------SLIKFSNIS 1041
                  I  E + +DL  E    +  E                        +L KF+ + 
Sbjct: 202  ------IGSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLR 255

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 1101
              +  ++ A  + G  S    +AH  + +     R T K  + L + LR  +++V   E+
Sbjct: 256  NSYQNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQER 315

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---- 1157
             I++  V    MP+  FI +F  NE N  W+D           IL  + P +++++    
Sbjct: 316  LIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQ----------ILASDKPYVEKIKLHEE 365

Query: 1158 ------QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
                   KL  ++ +  L +N+++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 366  DIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 425

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 426  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 485

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDE
Sbjct: 486  MIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDE 545

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED  +  P D+A   S+++  KD+L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 546  DSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 605

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 606  VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 642



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 311/624 (49%), Positives = 414/624 (66%), Gaps = 53/624 (8%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D +
Sbjct: 23  NPQSQLKLLVIRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 82

Query: 98  TLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            L LS+ T  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAK
Sbjct: 83  DLALSDETNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAK 142

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          + 
Sbjct: 143 RIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNADETAAPTATH- 201

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYE------------------------SLIKFSNIS 251
                 I  E + +DL  E    +  E                        +L KF+ + 
Sbjct: 202 ------IGSELAESDLEDEDNTDIDDEDEDEDEDGDSSSDSEEDVGIDPEMALEKFTQLR 255

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEK 311
             +  ++ A  + G  S    +AH  + +     R T K  + L + LR  +++V   E+
Sbjct: 256 NSYQNLQLAVNEHGRESAQTAQAHELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQER 315

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ---- 367
            I++  V    MP+  FI +F  NE N  W+D           IL  + P +++++    
Sbjct: 316 LIMKSAVEIAKMPKKSFIALFTGNESNEEWLDQ----------ILASDKPYVEKIKLHEE 365

Query: 368 ------QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
                  KL  ++ +  L +N+++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 366 DIRRSIAKLRAIEEETSLSVNNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT 425

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 426 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 485

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDE
Sbjct: 486 MIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDE 545

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED  +  P D+A   S+++  KD+L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 546 DSHLGDFIEDTTLELPLDSATATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 605

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKLR
Sbjct: 606 VGKQFDVTRERIRQIEAKALRKLR 629


>gi|359396018|ref|ZP_09189070.1| RNA polymerase sigma factor rpoD [Halomonas boliviensis LC1]
 gi|357970283|gb|EHJ92730.1| RNA polymerase sigma factor rpoD [Halomonas boliviensis LC1]
          Length = 616

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 317/607 (52%), Positives = 404/607 (66%), Gaps = 11/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   SDQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130  REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 1062
            E  L E    D   E  +    E           F+++R+       AF K G  S    
Sbjct: 190  ESELEEDVEGDSDDEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKHGRGSAELK 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250  SEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 1181
            P NE    W+D+    Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310  PGNESRKTWLDDFQAAQSKYADRLEPLRADIARAQRK-IAFEEDMVQLSVADLKEVNRKL 368

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489  RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 549  NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 608

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 609  PLRSFLD 615



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 310/594 (52%), Positives = 395/594 (66%), Gaps = 11/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  SDQSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130 REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 272
           E  L E    D   E  +    E           F+++R+       AF K G  S    
Sbjct: 190 ESELEEDVEGDSDDEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKHGRGSAELK 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250 SEQARLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 391
           P NE    W+D+    Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310 PGNESRKTWLDDFQAAQSKYADRLEPLRADIARAQRK-IAFEEDMVQLSVADLKEVNRKL 368

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489 RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|254237208|ref|ZP_04930531.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
 gi|126169139|gb|EAZ54650.1| sigma factor RpoD [Pseudomonas aeruginosa C3719]
          Length = 617

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 421/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130  REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 1010 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                    E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190  ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
                  ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250  TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310  FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490  RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 308/594 (51%), Positives = 412/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130 REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 220 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                   E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190 ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
                 ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250 TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310 FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490 RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|294634612|ref|ZP_06713146.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|451966365|ref|ZP_21919618.1| RNA polymerase sigma-D factor [Edwardsiella tarda NBRC 105688]
 gi|291091942|gb|EFE24503.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|451314666|dbj|GAC64980.1| RNA polymerase sigma-D factor [Edwardsiella tarda NBRC 105688]
          Length = 613

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/610 (50%), Positives = 416/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  +     +   ++      +        +  KF  +   ++K R A + EG +S
Sbjct: 183  SELPEEELNDDDDEDDDDEDGDDSDDDNSIDPELARQKFIELREQYEKTRLAIKAEGRSS 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                +   N+S      R   K  + L + +R  +++V   E+ I+++ V +  MP+ +F
Sbjct: 243  AKAQEEILNLSEIFKQFRLVPKQFDYLVNNMRAMMDRVRGQERLIMKLCVEQSKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE ++ W +    +   +   L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSITWFEAALAMGKPWGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 298/597 (49%), Positives = 407/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+   +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENIADEDAAEAAVQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++  +E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEASEARLSDLITGFVDPNAEEDMAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  +     +   ++      +        +  KF  +   ++K R A + EG +S
Sbjct: 183 SELPEEELNDDDDEDDDDEDGDDSDDDNSIDPELARQKFIELREQYEKTRLAIKAEGRSS 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
               +   N+S      R   K  + L + +R  +++V   E+ I+++ V +  MP+ +F
Sbjct: 243 AKAQEEILNLSEIFKQFRLVPKQFDYLVNNMRAMMDRVRGQERLIMKLCVEQSKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE ++ W +    +   +   L      ++   QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSITWFEAALAMGKPWGEKLKDMREEVERSLQKLHQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|338994482|ref|ZP_08635198.1| RNA polymerase sigma factor RpoD [Halomonas sp. TD01]
 gi|338766766|gb|EGP21682.1| RNA polymerase sigma factor RpoD [Halomonas sp. TD01]
          Length = 617

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 315/608 (51%), Positives = 402/608 (66%), Gaps = 12/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVVEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   SDHSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ A++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130  REVMSALAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEA 189

Query: 1010 EKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            E  L +        ++ +            E+  +F  I      +  AF K G  S   
Sbjct: 190  EPELSDDDIDSDEDDEDDDSTASEGGPDPEEAKARFEQIREQNAAVEAAFAKHGRGSAEL 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
                  ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK 
Sbjct: 250  KSEQARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKS 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRK 1180
            FP  E N  W+D   + Q  Y   L      I   Q+K I  + D+V L + DL+++NRK
Sbjct: 310  FPGYESNPKWLDTFQEAQPKYADRLEPLRADIARSQRK-IAFEEDMVQLTVADLKEVNRK 368

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 369  LSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 428

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  + 
Sbjct: 429  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELG 488

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    
Sbjct: 489  ERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEAT 548

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 549  RNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 608

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 609  EPLRSFLD 616



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 308/595 (51%), Positives = 393/595 (66%), Gaps = 12/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVVEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  SDHSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ A++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130 REVMSALAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEA 189

Query: 220 EKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           E  L +        ++ +            E+  +F  I      +  AF K G  S   
Sbjct: 190 EPELSDDDIDSDEDDEDDDSTASEGGPDPEEAKARFEQIREQNAAVEAAFAKHGRGSAEL 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
                 ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK 
Sbjct: 250 KSEQARLAELFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKS 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRK 390
           FP  E N  W+D   + Q  Y   L      I   Q+K I  + D+V L + DL+++NRK
Sbjct: 310 FPGYESNPKWLDTFQEAQPKYADRLEPLRADIARSQRK-IAFEEDMVQLTVADLKEVNRK 368

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 369 LSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 428

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  + 
Sbjct: 429 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELG 488

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    
Sbjct: 489 ERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEAT 548

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 RNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|444379032|ref|ZP_21178217.1| RNA polymerase sigma factor RpoD [Enterovibrio sp. AK16]
 gi|443676869|gb|ELT83565.1| RNA polymerase sigma factor RpoD [Enterovibrio sp. AK16]
          Length = 611

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/608 (50%), Positives = 423/608 (69%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM+S   +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMSETVADEDAVEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKG 1003
            IE+G+  +  +++  P +I  +L   DK+   E+++ +I+ G +D N    +     I  
Sbjct: 123  IEDGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDIISGFVDPNQEDIAPTATHIGS 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSES 1060
                 + +   +    D   E+ E    +  +   KF+++   ++ M+ + +K G   E 
Sbjct: 183  ELTEEQLEDEDDDGDDDDDDEEEEDTGIDPELAREKFNDLRLAYEGMQLSIQKNGRFHED 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
               A   +S      R   K  ++L + +R+ +++V   E+ ++ + V++  MP+  F++
Sbjct: 243  TAGAIAELSEVFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIVMRLCVDQAKMPKKTFVQ 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE + +W+D     +  Y   L +    ++   QKL  ++ +  L +  ++DI+R+
Sbjct: 303  LFSGNESSDSWLDEALASEKPYVDRLKQYEEDLRRCVQKLKIVEDETGLSVERVKDISRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   +++   
Sbjct: 483  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPMDSATMNNLKMAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  SEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  568 bits (1463), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/595 (50%), Positives = 414/595 (69%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM+S   +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMSETVADEDAVEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKG 213
           IE+G+  +  +++  P +I  +L   DK+   E+++ +I+ G +D N    +     I  
Sbjct: 123 IEDGINQVQVSVAEYPGSISSLLDQFDKVEAEELRLTDIISGFVDPNQEDIAPTATHIGS 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEKEGYNSES 270
                + +   +    D   E+ E    +  +   KF+++   ++ M+ + +K G   E 
Sbjct: 183 ELTEEQLEDEDDDGDDDDDDEEEEDTGIDPELAREKFNDLRLAYEGMQLSIQKNGRFHED 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
              A   +S      R   K  ++L + +R+ +++V   E+ ++ + V++  MP+  F++
Sbjct: 243 TAGAIAELSEVFKQFRLVPKQFDRLVNEMRDTMDRVRTQERIVMRLCVDQAKMPKKTFVQ 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE + +W+D     +  Y   L +    ++   QKL  ++ +  L +  ++DI+R+
Sbjct: 303 LFSGNESSDSWLDEALASEKPYVDRLKQYEEDLRRCVQKLKIVEDETGLSVERVKDISRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   +++   
Sbjct: 483 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPMDSATMNNLKMAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 SEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|292486903|ref|YP_003529773.1| RNA polymerase sigma-70 factor RpoD [Erwinia amylovora CFBP1430]
 gi|292900702|ref|YP_003540071.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|428783832|ref|ZP_19001325.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
            ACW56400]
 gi|291200550|emb|CBJ47679.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 gi|291552320|emb|CBA19364.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
            CFBP1430]
 gi|312170973|emb|CBX79232.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora ATCC
            BAA-2158]
 gi|426277547|gb|EKV55272.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
            ACW56400]
          Length = 614

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 304/611 (49%), Positives = 412/611 (67%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +       +    +      +    ++ I       KF+++   ++  R   + +  +
Sbjct: 183  VGSELSAEERDDDEDEDEESDDDSSDDDNSIDPELAREKFNDLRIQYETTRTVIKAKSRS 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +
Sbjct: 243  HADAIAEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W      +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFKAALAMNKPWSEKLNDVSEDVNRGLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  568 bits (1463), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 297/598 (49%), Positives = 403/598 (67%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +       +    +      +    ++ I       KF+++   ++  R   + +  +
Sbjct: 183 VGSELSAEERDDDEDEDEESDDDSSDDDNSIDPELAREKFNDLRIQYETTRTVIKAKSRS 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
               I    N+S+     R   K  + L +++R  +++V   E+ I+++ V  C MP+ +
Sbjct: 243 HADAIAEIQNLSDVFKQFRLVPKQFDFLVNSMRVMMDRVRTQERIIMKLCVELCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W      +   ++  L      +    QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFKAALAMNKPWSEKLNDVSEDVNRGLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           S   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 SATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|88704608|ref|ZP_01102321.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
 gi|88700929|gb|EAQ98035.1| RNA polymerase sigma factor rpoD [Congregibacter litoralis KT71]
          Length = 607

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 306/601 (50%), Positives = 414/601 (68%), Gaps = 10/601 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D + L+L
Sbjct: 10   RLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLIL 69

Query: 892  SNI--TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            ++   ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNN 1007
            G+++++ A++  P  +  +L     ++K E K+ +I+ G ++   +  S  ++ +     
Sbjct: 130  GIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADILVGYLNPADHVPSAQQIAEQQAAK 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                   E  +A    + +E  K     +F+ +   F+K  K   ++G   ++ IK    
Sbjct: 190  AAGNTDDEDDNAPTGPDPVEAKK-----RFTALKRQFNKTEKVLAEKGRQDKASIKEMEK 244

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            +       +FT K  + L D  R+ +  V + E++I+ IVV +C MPR  FI  F  NE 
Sbjct: 245  LGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRIVVRRCQMPRKEFITSFQGNES 304

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            N  W+    + + DY   L  +   I   Q+++  ++    L + ++++INR+M  GE +
Sbjct: 305  NAKWLSRHAR-KKDYGPKLNAHKEEIHRAQRQIGQIEEATGLTVTEIKEINRRMSMGEAR 363

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 364  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 423

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 424  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 483

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P D+A    ++   KD+L  L
Sbjct: 484  DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTIHSPIDSATGQGLQEATKDVLGGL 543

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 544  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFL 603

Query: 1428 E 1428
            +
Sbjct: 604  D 604



 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 303/596 (50%), Positives = 409/596 (68%), Gaps = 11/596 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D + L+L
Sbjct: 10  RLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLIL 69

Query: 102 SNI--TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           ++   ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNN 217
           G+++++ A++  P  +  +L     ++K E K+ +I+ G ++   +  S  ++ +     
Sbjct: 130 GIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADILVGYLNPADHVPSAQQIAEQQAAK 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
                  E  +A    + +E  K     +F+ +   F+K  K   ++G   ++ IK    
Sbjct: 190 AAGNTDDEDDNAPTGPDPVEAKK-----RFTALKRQFNKTEKVLAEKGRQDKASIKEMEK 244

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           +       +FT K  + L D  R+ +  V + E++I+ IVV +C MPR  FI  F  NE 
Sbjct: 245 LGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRIVVRRCQMPRKEFITSFQGNES 304

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           N  W+    + + DY   L  +   I   Q+++  ++    L + ++++INR+M  GE +
Sbjct: 305 NAKWLSRHAR-KKDYGPKLNAHKEEIHRAQRQIGQIEEATGLTVTEIKEINRRMSMGEAR 363

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 364 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 423

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 424 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 483

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P D+A    ++   KD+L  L
Sbjct: 484 DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTIHSPIDSATGQGLQEATKDVLGGL 543

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D+L
Sbjct: 544 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYL 599


>gi|441505117|ref|ZP_20987107.1| RNA polymerase sigma factor RpoD [Photobacterium sp. AK15]
 gi|441427218|gb|ELR64690.1| RNA polymerase sigma factor RpoD [Photobacterium sp. AK15]
          Length = 613

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/610 (50%), Positives = 417/610 (68%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPSAISHLLEQFDKVEADELRLTDIISGFVDPNEEETAAPTATHIG 182

Query: 1007 NN-EEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNS 1058
            +   E  L +        +  E+ + ++ I       KF  +   ++KM  A    G   
Sbjct: 183  SELSETDLEDEDKDLEEDDDSEESEEDTGIDPELAREKFMELRDSYEKMATAINTYGRTD 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                 A   +S+     R   K  ++L  +LR+ +++V   E+ I+ + V+   MP+  F
Sbjct: 243  ARTEVAVEELSDIFKQFRLIPKQFDRLISSLRDSMDRVRTNERLIMRMCVDNSKMPKKTF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            + +F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+
Sbjct: 303  VNLFAGNESSTDWIDEALNSGKPYAERLKNYEEELRRSVVKLRMLEEETGLSIERIKDIS 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA + ++R+
Sbjct: 483  LAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATSDNLRT 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSDVLRSFLD 612



 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/597 (50%), Positives = 408/597 (68%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P+ I  +L   DK+  +E+++ +I+ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPSAISHLLEQFDKVEADELRLTDIISGFVDPNEEETAAPTATHIG 182

Query: 217 NN-EEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNS 268
           +   E  L +        +  E+ + ++ I       KF  +   ++KM  A    G   
Sbjct: 183 SELSETDLEDEDKDLEEDDDSEESEEDTGIDPELAREKFMELRDSYEKMATAINTYGRTD 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
                A   +S+     R   K  ++L  +LR+ +++V   E+ I+ + V+   MP+  F
Sbjct: 243 ARTEVAVEELSDIFKQFRLIPKQFDRLISSLRDSMDRVRTNERLIMRMCVDNSKMPKKTF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           + +F  NE + +W+D        Y   L      ++    KL  L+ +  L +  ++DI+
Sbjct: 303 VNLFAGNESSTDWIDEALNSGKPYAERLKNYEEELRRSVVKLRMLEEETGLSIERIKDIS 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA + ++R+
Sbjct: 483 LAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLQLPMDAATSDNLRT 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|227329605|ref|ZP_03833629.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
            carotovorum WPP14]
          Length = 611

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 417/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ + EE    +    D   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183  VGSELSTEEMDDDDEEEDDEEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243  AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303  MFTGNETNNTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  568 bits (1463), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 408/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPNAEEDIAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ + EE    +    D   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183 VGSELSTEEMDDDDEEEDDEEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243 AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N  W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303 MFTGNETNNTWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|432515478|ref|ZP_19752694.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE224]
 gi|432700604|ref|ZP_19935749.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE169]
 gi|432747066|ref|ZP_19981728.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE43]
 gi|433145674|ref|ZP_20330810.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE168]
 gi|431039085|gb|ELD49971.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE224]
 gi|431241084|gb|ELF35531.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE169]
 gi|431290178|gb|ELF80903.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE43]
 gi|431659505|gb|ELJ26399.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE168]
          Length = 611

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 412/608 (67%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSES 1060
            +   +  ++    +   +        S+       KF+ +   +   R   + +G +  +
Sbjct: 183  SELSQEDLDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSHAA 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI 
Sbjct: 243  AQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFIT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303  LFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/595 (49%), Positives = 403/595 (67%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNSES 270
           +   +  ++    +   +        S+       KF+ +   +   R   + +G +  +
Sbjct: 183 SELSQEDLDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSHAA 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +FI 
Sbjct: 243 AQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFIT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303 LFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|51597716|ref|YP_071907.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
            32953]
 gi|108809138|ref|YP_653054.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|108810668|ref|YP_646435.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|150260325|ref|ZP_01917053.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|153950753|ref|YP_001399546.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
            31758]
 gi|165924959|ref|ZP_02220791.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. F1991016]
 gi|165937882|ref|ZP_02226443.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. IP275]
 gi|166008817|ref|ZP_02229715.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            E1979001]
 gi|166212040|ref|ZP_02238075.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            B42003004]
 gi|167399605|ref|ZP_02305129.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            UG05-0454]
 gi|167419320|ref|ZP_02311073.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. MG05-1020]
 gi|167425120|ref|ZP_02316873.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Mediaevalis
            str. K1973002]
 gi|170022885|ref|YP_001719390.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis YPIII]
 gi|186896860|ref|YP_001873972.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis PB1/+]
 gi|218927836|ref|YP_002345711.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|229837321|ref|ZP_04457484.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis Pestoides
            A]
 gi|229840533|ref|ZP_04460692.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
            Orientalis str. PEXU2]
 gi|229842919|ref|ZP_04463070.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
            Orientalis str. India 195]
 gi|229900861|ref|ZP_04515985.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis Nepal516]
 gi|294502714|ref|YP_003566776.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|384121147|ref|YP_005503767.1| RNA polymerase sigma factor RpoD [Yersinia pestis D106004]
 gi|384137370|ref|YP_005520072.1| RNA polymerase sigma factor RpoD [Yersinia pestis A1122]
 gi|384416294|ref|YP_005625656.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
            str. Harbin 35]
 gi|420545137|ref|ZP_15043298.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-01]
 gi|420550459|ref|ZP_15048053.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-02]
 gi|420555908|ref|ZP_15052904.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-03]
 gi|420561592|ref|ZP_15057856.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-04]
 gi|420566581|ref|ZP_15062363.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-05]
 gi|420572257|ref|ZP_15067516.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-06]
 gi|420577533|ref|ZP_15072283.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-07]
 gi|420582938|ref|ZP_15077210.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-08]
 gi|420588043|ref|ZP_15081812.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-09]
 gi|420593368|ref|ZP_15086608.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-10]
 gi|420599046|ref|ZP_15091692.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-11]
 gi|420604605|ref|ZP_15096656.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-12]
 gi|420609909|ref|ZP_15101468.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-13]
 gi|420615167|ref|ZP_15106141.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-14]
 gi|420620630|ref|ZP_15110920.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-15]
 gi|420625643|ref|ZP_15115462.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-16]
 gi|420630805|ref|ZP_15120148.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-19]
 gi|420635985|ref|ZP_15124775.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-25]
 gi|420641576|ref|ZP_15129822.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-29]
 gi|420645734|ref|ZP_15133639.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-32]
 gi|420646671|ref|ZP_15134487.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-32]
 gi|420652359|ref|ZP_15139592.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-34]
 gi|420657805|ref|ZP_15144501.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-36]
 gi|420663139|ref|ZP_15149264.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-42]
 gi|420668188|ref|ZP_15153835.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-45]
 gi|420673425|ref|ZP_15158597.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-46]
 gi|420678934|ref|ZP_15163605.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-47]
 gi|420684161|ref|ZP_15168306.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-48]
 gi|420689373|ref|ZP_15172932.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-52]
 gi|420695170|ref|ZP_15177999.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-53]
 gi|420700448|ref|ZP_15182584.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-54]
 gi|420706579|ref|ZP_15187474.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-55]
 gi|420711871|ref|ZP_15192266.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-56]
 gi|420717235|ref|ZP_15197011.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-58]
 gi|420722874|ref|ZP_15201825.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-59]
 gi|420728515|ref|ZP_15206843.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-60]
 gi|420733623|ref|ZP_15211443.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-61]
 gi|420742814|ref|ZP_15219723.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-63]
 gi|420744309|ref|ZP_15221025.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-64]
 gi|420750219|ref|ZP_15226022.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-65]
 gi|420755311|ref|ZP_15230537.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-66]
 gi|420761344|ref|ZP_15235363.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-71]
 gi|420766547|ref|ZP_15240071.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-72]
 gi|420771565|ref|ZP_15244566.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-76]
 gi|420776906|ref|ZP_15249377.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-88]
 gi|420782396|ref|ZP_15254188.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-89]
 gi|420787810|ref|ZP_15258944.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-90]
 gi|420793284|ref|ZP_15263875.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-91]
 gi|420798438|ref|ZP_15268504.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-92]
 gi|420803807|ref|ZP_15273341.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-93]
 gi|420808997|ref|ZP_15278038.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-94]
 gi|420814754|ref|ZP_15283195.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-95]
 gi|420819937|ref|ZP_15287890.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-96]
 gi|420825005|ref|ZP_15292428.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-98]
 gi|420830798|ref|ZP_15297652.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-99]
 gi|420835598|ref|ZP_15301985.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-100]
 gi|420840769|ref|ZP_15306670.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-101]
 gi|420846360|ref|ZP_15311728.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-102]
 gi|420851717|ref|ZP_15316486.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-103]
 gi|420857281|ref|ZP_15321187.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-113]
 gi|421762074|ref|ZP_16198873.1| RNA polymerase sigma factor RpoD [Yersinia pestis INS]
 gi|51590998|emb|CAH22656.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
            32953]
 gi|108774316|gb|ABG16835.1| RNA polymerase sigma factor RpoD [Yersinia pestis Nepal516]
 gi|108781051|gb|ABG15109.1| RNA polymerase sigma factor RpoD [Yersinia pestis Antiqua]
 gi|115346447|emb|CAL19320.1| RNA polymerase sigma factor RpoD [Yersinia pestis CO92]
 gi|149289733|gb|EDM39810.1| RNA polymerase sigma factor RpoD [Yersinia pestis CA88-4125]
 gi|152962248|gb|ABS49709.1| RNA polymerase sigma factor RpoD [Yersinia pseudotuberculosis IP
            31758]
 gi|165914294|gb|EDR32910.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. IP275]
 gi|165923159|gb|EDR40310.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. F1991016]
 gi|165992156|gb|EDR44457.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            E1979001]
 gi|166206786|gb|EDR51266.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            B42003004]
 gi|166963314|gb|EDR59335.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Orientalis
            str. MG05-1020]
 gi|167052109|gb|EDR63517.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Antiqua str.
            UG05-0454]
 gi|167055883|gb|EDR65664.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Mediaevalis
            str. K1973002]
 gi|169749419|gb|ACA66937.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
            YPIII]
 gi|186699886|gb|ACC90515.1| RNA polymerase, sigma 70 subunit, RpoD [Yersinia pseudotuberculosis
            PB1/+]
 gi|229682200|gb|EEO78292.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis Nepal516]
 gi|229689985|gb|EEO82043.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
            Orientalis str. India 195]
 gi|229696899|gb|EEO86946.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis biovar
            Orientalis str. PEXU2]
 gi|229705444|gb|EEO91454.1| RNA polymerase, sigma 70 (sigma D) factor [Yersinia pestis Pestoides
            A]
 gi|262360743|gb|ACY57464.1| RNA polymerase sigma factor RpoD [Yersinia pestis D106004]
 gi|294353173|gb|ADE63514.1| RNA polymerase sigma factor RpoD [Yersinia pestis Z176003]
 gi|320016798|gb|ADW00370.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
            str. Harbin 35]
 gi|342852499|gb|AEL71052.1| RNA polymerase sigma factor RpoD [Yersinia pestis A1122]
 gi|391431789|gb|EIQ93302.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-01]
 gi|391432834|gb|EIQ94237.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-02]
 gi|391435491|gb|EIQ96543.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-03]
 gi|391447728|gb|EIR07610.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-04]
 gi|391448734|gb|EIR08518.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-05]
 gi|391451400|gb|EIR10898.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-06]
 gi|391464064|gb|EIR22399.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-07]
 gi|391465468|gb|EIR23662.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-08]
 gi|391467540|gb|EIR25511.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-09]
 gi|391480808|gb|EIR37410.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-10]
 gi|391481664|gb|EIR38175.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-11]
 gi|391481894|gb|EIR38386.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-12]
 gi|391496213|gb|EIR51190.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-13]
 gi|391496689|gb|EIR51608.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-15]
 gi|391500261|gb|EIR54783.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-14]
 gi|391511814|gb|EIR65185.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-16]
 gi|391513573|gb|EIR66776.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-19]
 gi|391515669|gb|EIR68635.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-25]
 gi|391527286|gb|EIR79209.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-29]
 gi|391530172|gb|EIR81781.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-34]
 gi|391531336|gb|EIR82835.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-32]
 gi|391533909|gb|EIR85147.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-32]
 gi|391544361|gb|EIR94588.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-36]
 gi|391545951|gb|EIR95986.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-42]
 gi|391546747|gb|EIR96708.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-45]
 gi|391560552|gb|EIS09166.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-46]
 gi|391561742|gb|EIS10244.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-47]
 gi|391563756|gb|EIS12029.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-48]
 gi|391575940|gb|EIS22578.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-52]
 gi|391576638|gb|EIS23167.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-53]
 gi|391588175|gb|EIS33247.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-55]
 gi|391590602|gb|EIS35302.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-54]
 gi|391591865|gb|EIS36378.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-56]
 gi|391605108|gb|EIS48034.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-60]
 gi|391606483|gb|EIS49210.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-58]
 gi|391607350|gb|EIS49958.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-59]
 gi|391609965|gb|EIS52310.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-63]
 gi|391619331|gb|EIS60607.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-61]
 gi|391628485|gb|EIS68557.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-64]
 gi|391630913|gb|EIS70606.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-65]
 gi|391642186|gb|EIS80491.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-71]
 gi|391644910|gb|EIS82854.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-72]
 gi|391647145|gb|EIS84808.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-66]
 gi|391654695|gb|EIS91510.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-76]
 gi|391661397|gb|EIS97446.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-88]
 gi|391666310|gb|EIT01794.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-89]
 gi|391668155|gb|EIT03416.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-90]
 gi|391672553|gb|EIT07356.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-91]
 gi|391685839|gb|EIT19327.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-93]
 gi|391687304|gb|EIT20634.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-92]
 gi|391688459|gb|EIT21669.1| RNA polymerase sigma factor RpoD [Yersinia pestis PY-94]
 gi|391700021|gb|EIT32153.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-95]
 gi|391703361|gb|EIT35131.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-96]
 gi|391704174|gb|EIT35853.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-98]
 gi|391714224|gb|EIT44901.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-99]
 gi|391719819|gb|EIT49891.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-100]
 gi|391720252|gb|EIT50291.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-101]
 gi|391730936|gb|EIT59698.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-102]
 gi|391733427|gb|EIT61814.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-103]
 gi|391737020|gb|EIT64946.1| RNA polymerase sigma factor rpoD [Yersinia pestis PY-113]
 gi|411177615|gb|EKS47628.1| RNA polymerase sigma factor RpoD [Yersinia pestis INS]
          Length = 612

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 314/630 (49%), Positives = 423/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 1045
                EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 172  ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 228

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 1098
              R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229  NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 281

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
             E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 282  QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462  LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 307/617 (49%), Positives = 414/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 255
               EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 172 ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 228

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 308
             R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229 NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 281

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
            E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 282 QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|52425815|ref|YP_088952.1| RNA polymerase sigma factor RpoD [Mannheimia succiniciproducens
            MBEL55E]
 gi|52307867|gb|AAU38367.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 628

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 308/620 (49%), Positives = 418/620 (67%), Gaps = 23/620 (3%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 12   NPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLESAPDAD 71

Query: 888  TLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
             LMLS   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKR
Sbjct: 72   DLMLSETIADEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKR 130

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG--- 1003
            IE+G+ ++  A++  P  +  +L   +++ +  +++ +++ G +D N    +  I     
Sbjct: 131  IEDGINEVQSAVAEYPEALDYLLKQYEQVEEGSVRLADLITGFVDLNAEEASEEISDLEE 190

Query: 1004 --------------NKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMR 1048
                          N    +E+     +S D S   ++ ++  E   KFS +     K  
Sbjct: 191  VLDDEDGDIPADALNDEEEDEESDEGDTSTDDSDNSIDPEVARE---KFSALKDQCVKTL 247

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
            +  EK G       +    +S+     R   +  + L  ++R+ + QV   E+QI  + V
Sbjct: 248  EFIEKYGRTDNKVKEQIQVLSDIFTQFRLVPRQFDTLVLSMRSMMKQVRAEERQIQRLAV 307

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
            +   +P+  F K F  NE +  W+++  + +  Y   L +  P I +   +L  ++TD  
Sbjct: 308  DYAKVPKDDFQKAFIGNETSEQWLESLLQSKKTYVEKLQQRAPEISKSIVRLQQVETDTK 367

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  +RDI  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 368  LTVQQIRDIGERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 427

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 428  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 487

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 488  EMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPL 547

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 548  DSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 607

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   L+ FL+
Sbjct: 608  KALRKLRHPSRSETLRSFLD 627



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 301/607 (49%), Positives = 409/607 (67%), Gaps = 23/607 (3%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 12  NPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLESAPDAD 71

Query: 98  TLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
            LMLS   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKR
Sbjct: 72  DLMLSETIADEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKR 130

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG--- 213
           IE+G+ ++  A++  P  +  +L   +++ +  +++ +++ G +D N    +  I     
Sbjct: 131 IEDGINEVQSAVAEYPEALDYLLKQYEQVEEGSVRLADLITGFVDLNAEEASEEISDLEE 190

Query: 214 --------------NKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMR 258
                         N    +E+     +S D S   ++ ++  E   KFS +     K  
Sbjct: 191 VLDDEDGDIPADALNDEEEDEESDEGDTSTDDSDNSIDPEVARE---KFSALKDQCVKTL 247

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
           +  EK G       +    +S+     R   +  + L  ++R+ + QV   E+QI  + V
Sbjct: 248 EFIEKYGRTDNKVKEQIQVLSDIFTQFRLVPRQFDTLVLSMRSMMKQVRAEERQIQRLAV 307

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
           +   +P+  F K F  NE +  W+++  + +  Y   L +  P I +   +L  ++TD  
Sbjct: 308 DYAKVPKDDFQKAFIGNETSEQWLESLLQSKKTYVEKLQQRAPEISKSIVRLQQVETDTK 367

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  +RDI  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 368 LTVQQIRDIGERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 427

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 428 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 487

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 488 EMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPL 547

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 548 DSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 607

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 608 KALRKLR 614


>gi|333894440|ref|YP_004468315.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
 gi|332994458|gb|AEF04513.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 608

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 310/600 (51%), Positives = 414/600 (69%), Gaps = 3/600 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D++ L++
Sbjct: 8    QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDSDELLM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68   QEATADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   D     EI+I +I+ G +D N   +      +  +   +
Sbjct: 128  NQVQCSVAEYPEAITYLLDQWDLYEAEEIRISDIISGFVDPNDDQDLAPTATHIGSELSE 187

Query: 1012 ILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 1068
              +E    D   E  ++   +   +  KF  +   + K R   EK+G +  +  +  N +
Sbjct: 188  EELEDEDDDDDEEDEDEGGVDPELARAKFGALRDQYIKARDVIEKKGRSHAAAREQINAL 247

Query: 1069 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 1128
            S      R   K  +++   +R+ +++V   E+ +++  V    MP+  FIK F  NE +
Sbjct: 248  SEVFKEFRLVPKQFDRMVKNMRSMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGNETS 307

Query: 1129 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
              W+    K    Y+  L  N   I+    K+  ++ +  L + D++DINR+M  GE KA
Sbjct: 308  SAWLTKAIKANAAYSDALAVNKEEIERCISKMNQVEQETGLVIADIKDINRRMSIGEAKA 367

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 368  RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 427

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M MPE+
Sbjct: 428  WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED 487

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L  LT
Sbjct: 488  KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEVLAGLT 547

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ FL+
Sbjct: 548  AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFLD 607



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 303/587 (51%), Positives = 404/587 (68%), Gaps = 3/587 (0%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D++ L++
Sbjct: 8   QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDSDELLM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68  QEATADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   D     EI+I +I+ G +D N   +      +  +   +
Sbjct: 128 NQVQCSVAEYPEAITYLLDQWDLYEAEEIRISDIISGFVDPNDDQDLAPTATHIGSELSE 187

Query: 222 ILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278
             +E    D   E  ++   +   +  KF  +   + K R   EK+G +  +  +  N +
Sbjct: 188 EELEDEDDDDDEEDEDEGGVDPELARAKFGALRDQYIKARDVIEKKGRSHAAAREQINAL 247

Query: 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 338
           S      R   K  +++   +R+ +++V   E+ +++  V    MP+  FIK F  NE +
Sbjct: 248 SEVFKEFRLVPKQFDRMVKNMRSMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGNETS 307

Query: 339 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
             W+    K    Y+  L  N   I+    K+  ++ +  L + D++DINR+M  GE KA
Sbjct: 308 SAWLTKAIKANAAYSDALAVNKEEIERCISKMNQVEQETGLVIADIKDINRRMSIGEAKA 367

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 368 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 427

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M MPE+
Sbjct: 428 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED 487

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L  LT
Sbjct: 488 KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEVLAGLT 547

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|15595773|ref|NP_249267.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|116054304|ref|YP_788749.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218889317|ref|YP_002438181.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|254243670|ref|ZP_04936992.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|296387081|ref|ZP_06876580.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAb1]
 gi|313111780|ref|ZP_07797573.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
 gi|355646993|ref|ZP_09054746.1| RNA polymerase sigma factor rpoD [Pseudomonas sp. 2_1_26]
 gi|386056646|ref|YP_005973168.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa M18]
 gi|386068504|ref|YP_005983808.1| RNA polymerase sigma factor [Pseudomonas aeruginosa NCGM2.S1]
 gi|392981989|ref|YP_006480576.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa DK2]
 gi|416855772|ref|ZP_11911693.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 138244]
 gi|416873044|ref|ZP_11917171.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 152504]
 gi|418590805|ref|ZP_13154710.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa MPAO1/P2]
 gi|419756058|ref|ZP_14282410.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PADK2_CF510]
 gi|420137171|ref|ZP_14645166.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa CIG1]
 gi|421151662|ref|ZP_15611270.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 14886]
 gi|421157616|ref|ZP_15616973.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 25324]
 gi|421165454|ref|ZP_15623782.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 700888]
 gi|421172341|ref|ZP_15630116.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa CI27]
 gi|421178488|ref|ZP_15636101.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa E2]
 gi|421515196|ref|ZP_15961882.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAO579]
 gi|424942999|ref|ZP_18358762.1| sigma factor RpoD [Pseudomonas aeruginosa NCMG1179]
 gi|451983567|ref|ZP_21931846.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 18A]
 gi|133310|sp|P26480.1|RPOD_PSEAE RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|9946447|gb|AAG03965.1|AE004494_1 sigma factor RpoD [Pseudomonas aeruginosa PAO1]
 gi|216913|dbj|BAA14146.1| principal sigma factor [Pseudomonas aeruginosa]
 gi|30060254|gb|AAP13091.1| RpoD [Pseudomonas sp. M18]
 gi|115589525|gb|ABJ15540.1| sigma factor RpoD [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126197048|gb|EAZ61111.1| sigma factor RpoD [Pseudomonas aeruginosa 2192]
 gi|218769540|emb|CAW25300.1| sigma factor RpoD [Pseudomonas aeruginosa LESB58]
 gi|310884075|gb|EFQ42669.1| sigma factor RpoD [Pseudomonas aeruginosa 39016]
 gi|334842670|gb|EGM21273.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 138244]
 gi|334845342|gb|EGM23905.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 152504]
 gi|346059445|dbj|GAA19328.1| sigma factor RpoD [Pseudomonas aeruginosa NCMG1179]
 gi|347302952|gb|AEO73066.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa M18]
 gi|348037063|dbj|BAK92423.1| RNA polymerase sigma factor [Pseudomonas aeruginosa NCGM2.S1]
 gi|354828135|gb|EHF12262.1| RNA polymerase sigma factor rpoD [Pseudomonas sp. 2_1_26]
 gi|375050351|gb|EHS42833.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa MPAO1/P2]
 gi|384397720|gb|EIE44131.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PADK2_CF510]
 gi|392317494|gb|AFM62874.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa DK2]
 gi|403250012|gb|EJY63473.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa CIG1]
 gi|404348924|gb|EJZ75261.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PAO579]
 gi|404526862|gb|EKA37049.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 14886]
 gi|404537937|gb|EKA47500.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa CI27]
 gi|404541667|gb|EKA51018.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 700888]
 gi|404548337|gb|EKA57292.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa E2]
 gi|404550423|gb|EKA59172.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa ATCC 25324]
 gi|451758806|emb|CCQ84369.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa 18A]
 gi|453045958|gb|EME93676.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa PA21_ST175]
          Length = 617

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 420/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130  REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 1010 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                    E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190  ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
                  ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250  TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310  FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490  RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 308/594 (51%), Positives = 411/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130 REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 220 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                   E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190 ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
                 ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250 TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310 FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490 RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|410087073|ref|ZP_11283778.1| RNA polymerase sigma factor RpoD [Morganella morganii SC01]
 gi|409766302|gb|EKN50396.1| RNA polymerase sigma factor RpoD [Morganella morganii SC01]
          Length = 616

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/625 (49%), Positives = 414/625 (66%), Gaps = 35/625 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENSTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N   +      N
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLITGFVDPNAEEDLAPTATN 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 1043
                          ++L  E+L K   +                        KF  +   
Sbjct: 183  ------------IGSELPAEELNKDDDDEDEDEEEDSDSDDDNSIDPELARQKFEALRVQ 230

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
             +K R+  +  G +  +       +S      R   K  + L + +R  +++V Q E+ I
Sbjct: 231  HEKARQQIKIHGRDHPNTNAEIQQLSEVFKEFRLVPKQFDHLVNNMREMMDRVRQQERYI 290

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            +++ V +  MP+ +FI +F  NE + +W      +   ++  L      ++   Q+L  +
Sbjct: 291  MKLCVEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKPWSEKLQDVAEEVERSLQRLRQI 350

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 351  EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 410

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 411  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 470

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 471  RQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 530

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 531  LELPLDSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 590

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  RQIEAKALRKLRHPSRSEVLRSFLD 615



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 300/612 (49%), Positives = 405/612 (66%), Gaps = 35/612 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENSTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N   +      N
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLITGFVDPNAEEDLAPTATN 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 253
                         ++L  E+L K   +                        KF  +   
Sbjct: 183 ------------IGSELPAEELNKDDDDEDEDEEEDSDSDDDNSIDPELARQKFEALRVQ 230

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
            +K R+  +  G +  +       +S      R   K  + L + +R  +++V Q E+ I
Sbjct: 231 HEKARQQIKIHGRDHPNTNAEIQQLSEVFKEFRLVPKQFDHLVNNMREMMDRVRQQERYI 290

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           +++ V +  MP+ +FI +F  NE + +W      +   ++  L      ++   Q+L  +
Sbjct: 291 MKLCVEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKPWSEKLQDVAEEVERSLQRLRQI 350

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 351 EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 410

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 411 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 470

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 471 RQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 530

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 531 LELPLDSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 590

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 591 RQIEAKALRKLR 602


>gi|421492843|ref|ZP_15940202.1| RPOD [Morganella morganii subsp. morganii KT]
 gi|455740446|ref|YP_007506712.1| RNA polymerase sigma factor RpoD [Morganella morganii subsp. morganii
            KT]
 gi|400192948|gb|EJO26085.1| RPOD [Morganella morganii subsp. morganii KT]
 gi|455422009|gb|AGG32339.1| RNA polymerase sigma factor RpoD [Morganella morganii subsp. morganii
            KT]
          Length = 616

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/625 (49%), Positives = 414/625 (66%), Gaps = 35/625 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENSTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N   +      N
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLITGFVDPNAEEDLAPTATN 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 1043
                          ++L  E+L K   +                        KF  +   
Sbjct: 183  ------------IGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPELARQKFEALRVQ 230

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
             +K R+  +  G +  +       +S      R   K  + L + +R  +++V Q E+ I
Sbjct: 231  HEKARQQIKIHGRDHPNTNAEIQQLSEVFKEFRLVPKQFDHLVNNMREMMDRVRQQERYI 290

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            +++ V +  MP+ +FI +F  NE + +W      +   ++  L      ++   Q+L  +
Sbjct: 291  MKLCVEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKPWSEKLQDVAEEVERSLQRLRQI 350

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 351  EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 410

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 411  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 470

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 471  RQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 530

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 531  LELPLDSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 590

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  RQIEAKALRKLRHPSRSEVLRSFLD 615



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 300/612 (49%), Positives = 405/612 (66%), Gaps = 35/612 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +  +DDD  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENSTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E+++ +++ G +D N   +      N
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGEVRLSDLITGFVDPNAEEDLAPTATN 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 253
                         ++L  E+L K   +                        KF  +   
Sbjct: 183 ------------IGSELPAEELNKDDDDEDEEEEDDSDSDDDNSIDPELARQKFEALRVQ 230

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
            +K R+  +  G +  +       +S      R   K  + L + +R  +++V Q E+ I
Sbjct: 231 HEKARQQIKIHGRDHPNTNAEIQQLSEVFKEFRLVPKQFDHLVNNMREMMDRVRQQERYI 290

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           +++ V +  MP+ +FI +F  NE + +W      +   ++  L      ++   Q+L  +
Sbjct: 291 MKLCVEQSKMPKKNFITLFTGNETSDSWFTAAVAMNKPWSEKLQDVAEEVERSLQRLRQI 350

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 351 EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 410

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 411 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 470

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 471 RQMLQEMGREPSPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 530

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A + S+RS   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 531 LELPLDSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 590

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 591 RQIEAKALRKLR 602


>gi|372270823|ref|ZP_09506871.1| RNA polymerase sigma factor RpoD [Marinobacterium stanieri S30]
          Length = 613

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 311/604 (51%), Positives = 419/604 (69%), Gaps = 8/604 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D E L+L
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIRVSEEAPDAEDLLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   S ++ +E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 70   SGGDSAEEADEEAVAALAAVENDAGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS-----SNNRVIKGNKN 1006
            ++++ A+S  P ++  IL A + + + E ++ +I  G ID +       +   V     +
Sbjct: 130  REVMMALSRFPGSVDIILDAYNSVLQEEGRLSDIFSGYIDPDSDIPAPEAEAPVEIEEDD 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLK--YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            ++E+    +    D S E+ E+     E+  +F  I    D +     + G   E    A
Sbjct: 190  DDEDDDDDKEKGDDDSNEEKERGPDPEEARQRFGLIQESLDNLNATIARGGSADEVEFAA 249

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
             + ++N    I+ + +  + L   +R+ I+ + + E+ I+ I   +  MPR  FIK FP 
Sbjct: 250  MS-LANAFAPIKLSPRYYDLLVQRVRDCIDSIRKQERTIMRICTQRAKMPRPLFIKSFPG 308

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE +  W+D        +   + R++P ++  Q++L  ++ +I L L D++++NR +  G
Sbjct: 309  NETSQEWLDELVNSDKPFAAPIKRSMPDLQRAQRRLRQVEENIGLRLADIKEVNRDLSIG 368

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 369  EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +ME
Sbjct: 429  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERME 488

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D A    +R   ++IL
Sbjct: 489  MPEDKIRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTLHSPVDTATGEGLRESTREIL 548

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
            + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+
Sbjct: 549  SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLR 608

Query: 1425 IFLE 1428
             F++
Sbjct: 609  TFID 612



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/591 (51%), Positives = 410/591 (69%), Gaps = 8/591 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I VSE   D E L+L
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIRMINDMGIRVSEEAPDAEDLLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   S ++ +E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 70  SGGDSAEEADEEAVAALAAVENDAGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS-----SNNRVIKGNKN 216
           ++++ A+S  P ++  IL A + + + E ++ +I  G ID +       +   V     +
Sbjct: 130 REVMMALSRFPGSVDIILDAYNSVLQEEGRLSDIFSGYIDPDSDIPAPEAEAPVEIEEDD 189

Query: 217 NNEEKILIESSSADLSTEQLEKLK--YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           ++E+    +    D S E+ E+     E+  +F  I    D +     + G   E    A
Sbjct: 190 DDEDDDDDKEKGDDDSNEEKERGPDPEEARQRFGLIQESLDNLNATIARGGSADEVEFAA 249

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
            + ++N    I+ + +  + L   +R+ I+ + + E+ I+ I   +  MPR  FIK FP 
Sbjct: 250 MS-LANAFAPIKLSPRYYDLLVQRVRDCIDSIRKQERTIMRICTQRAKMPRPLFIKSFPG 308

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NE +  W+D        +   + R++P ++  Q++L  ++ +I L L D++++NR +  G
Sbjct: 309 NETSQEWLDELVNSDKPFAAPIKRSMPDLQRAQRRLRQVEENIGLRLADIKEVNRDLSIG 368

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 369 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +ME
Sbjct: 429 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERME 488

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+KIRK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D A    +R   ++IL
Sbjct: 489 MPEDKIRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTLHSPVDTATGEGLRESTREIL 548

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           + LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|308050979|ref|YP_003914545.1| RNA polymerase sigma-70 subunit RpoD [Ferrimonas balearica DSM 9799]
 gi|307633169|gb|ADN77471.1| RNA polymerase, sigma 70 subunit, RpoD [Ferrimonas balearica DSM
            9799]
          Length = 610

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 307/611 (50%), Positives = 413/611 (67%), Gaps = 19/611 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + L
Sbjct: 6    QSQLKLLVAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIQVFESAPDQDEL 65

Query: 890  MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            M+S   +D+D  EA   AL++V+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIE+
Sbjct: 66   MMSEDATDEDAAEAAAQALASVEGELGRTTDPVRMYMREMGTVELLTREGEILIAKRIED 125

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK---- 1005
            G+  +  +I+  P  I  +L   D+    EI++ EI+ G + +   +      G++    
Sbjct: 126  GINQVQCSIAEYPEAISFLLDQWDRFEAEEIRLAEIISGFVTEEEEAPTATHVGSELPKE 185

Query: 1006 --------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                       ++    + +S     EQ  +       KF+++  H++ ++KAF + G +
Sbjct: 186  ELDDEDEDEEEDDDDSDDDTSNGPDPEQARE-------KFTSLREHYELVQKAFAEHGRD 238

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S         +S      R   K  + L + +R+ +++V   E+ I+++ V +  MP+ +
Sbjct: 239  SLEAAMLITRLSELFKEFRLVPKQFDVLVNNMRSMMDRVRVQERLIMKMCVEQAKMPKKN 298

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K+F  +E    W+  E      Y+  L  +   +    QKL  +Q +  L +  ++DI
Sbjct: 299  FLKLFAGHESETAWLQAEIDAGKSYSAALGEHQEELHRCIQKLAQIQEETGLSIAKIKDI 358

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 359  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 418

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 419  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 478

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S++
Sbjct: 479  ELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAQPVDSATAESLK 538

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   ++L  LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 539  AATAEVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 598

Query: 1418 SRYYKLKIFLE 1428
            SR   LK FL+
Sbjct: 599  SRSEILKSFLD 609



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 404/598 (67%), Gaps = 19/598 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + L
Sbjct: 6   QSQLKLLVAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIQVFESAPDQDEL 65

Query: 100 MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           M+S   +D+D  EA   AL++V+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIE+
Sbjct: 66  MMSEDATDEDAAEAAAQALASVEGELGRTTDPVRMYMREMGTVELLTREGEILIAKRIED 125

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK---- 215
           G+  +  +I+  P  I  +L   D+    EI++ EI+ G + +   +      G++    
Sbjct: 126 GINQVQCSIAEYPEAISFLLDQWDRFEAEEIRLAEIISGFVTEEEEAPTATHVGSELPKE 185

Query: 216 --------NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                      ++    + +S     EQ  +       KF+++  H++ ++KAF + G +
Sbjct: 186 ELDDEDEDEEEDDDDSDDDTSNGPDPEQARE-------KFTSLREHYELVQKAFAEHGRD 238

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S         +S      R   K  + L + +R+ +++V   E+ I+++ V +  MP+ +
Sbjct: 239 SLEAAMLITRLSELFKEFRLVPKQFDVLVNNMRSMMDRVRVQERLIMKMCVEQAKMPKKN 298

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K+F  +E    W+  E      Y+  L  +   +    QKL  +Q +  L +  ++DI
Sbjct: 299 FLKLFAGHESETAWLQAEIDAGKSYSAALGEHQEELHRCIQKLAQIQEETGLSIAKIKDI 358

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 359 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 418

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 419 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 478

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S++
Sbjct: 479 ELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLAQPVDSATAESLK 538

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   ++L  LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 539 AATAEVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 596


>gi|33151868|ref|NP_873221.1| RNA polymerase sigma factor RpoD [Haemophilus ducreyi 35000HP]
 gi|33148089|gb|AAP95610.1| RNA polymerase sigma factor [Haemophilus ducreyi 35000HP]
          Length = 613

 Score =  581 bits (1497), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/617 (50%), Positives = 421/617 (68%), Gaps = 26/617 (4%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 4    QSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDEL 63

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 64   MLAENIADEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 122

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
            EG+ ++  A++  P  + E++    ++ +  +++ ++V   +D N  +   V++ + + +
Sbjct: 123  EGINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQAEEDVVELDSDLD 182

Query: 1009 EEKILI------------ESSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKE 1054
            EE   +               SAD + +     +L  E   KF  +    +K  +A +K 
Sbjct: 183  EEASDVVADVDDENEDEESDGSADNTDDNSIDPELARE---KFYALREQHEKALQAIQKH 239

Query: 1055 GYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            G +   S+ +I+A ++I  E    R   K  + L ++++  + QV   E+QI    V   
Sbjct: 240  GRSHKKSKQHIQALSDIFRE---FRLVPKQFDLLVESMQRMMKQVRAEERQIQRYAVEYA 296

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             M +  F+K+F  NE +  W+D     +      L   +  I+     L  ++ D  L +
Sbjct: 297  QMKKADFLKLFQGNETSEEWIDKAINARKGAAPKLANYVEQIRINISNLQRMEQDTDLTV 356

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              +R+I  ++ +GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 357  AQIREIGGRIASGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 416

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G
Sbjct: 417  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMG 476

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD DSHLGDFI+DEN+  P D+A
Sbjct: 477  REATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDD-DSHLGDFIQDENLELPLDSA 535

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 536  TAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 596  RKLRHPSRSETLRSFLD 612



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 412/604 (68%), Gaps = 26/604 (4%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 4   QSQLELLIAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDEL 63

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 64  MLAENIADEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 122

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
           EG+ ++  A++  P  + E++    ++ +  +++ ++V   +D N  +   V++ + + +
Sbjct: 123 EGINEVQCAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQAEEDVVELDSDLD 182

Query: 219 EEKILI------------ESSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKE 264
           EE   +               SAD + +     +L  E   KF  +    +K  +A +K 
Sbjct: 183 EEASDVVADVDDENEDEESDGSADNTDDNSIDPELARE---KFYALREQHEKALQAIQKH 239

Query: 265 GYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           G +   S+ +I+A ++I  E    R   K  + L ++++  + QV   E+QI    V   
Sbjct: 240 GRSHKKSKQHIQALSDIFRE---FRLVPKQFDLLVESMQRMMKQVRAEERQIQRYAVEYA 296

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            M +  F+K+F  NE +  W+D     +      L   +  I+     L  ++ D  L +
Sbjct: 297 QMKKADFLKLFQGNETSEEWIDKAINARKGAAPKLANYVEQIRINISNLQRMEQDTDLTV 356

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             +R+I  ++ +GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 357 AQIREIGGRIASGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 416

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G
Sbjct: 417 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMG 476

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD DSHLGDFI+DEN+  P D+A
Sbjct: 477 REATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDD-DSHLGDFIQDENLELPLDSA 535

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 536 TAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 622 RKLR 625
           RKLR
Sbjct: 596 RKLR 599


>gi|422804094|ref|ZP_16852526.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
 gi|324115354|gb|EGC09318.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
          Length = 613

 Score =  581 bits (1497), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KFS +   ++  R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFSELRAQYEVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KFS +   ++  R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFSELRAQYEVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|269103529|ref|ZP_06156226.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
            damselae CIP 102761]
 gi|268163427|gb|EEZ41923.1| RNA polymerase sigma factor RpoD [Photobacterium damselae subsp.
            damselae CIP 102761]
          Length = 619

 Score =  581 bits (1497), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 313/631 (49%), Positives = 419/631 (66%), Gaps = 44/631 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I ++L   DK+  +E+++ +I               I G  +
Sbjct: 123  IEDGINQVQCSVAEYPKAISQLLDMFDKVEADELRLTDI---------------ISGFVD 167

Query: 1007 NNEEKILIESSS---ADLSTEQLEKLKYESLI--------------------------KF 1037
             NEE+    +++   ++LS   LE    +                             KF
Sbjct: 168  PNEEETAAPTATHIGSELSESDLEDEDRDLDEDEDEDEDGDSSDDSDDNNIDPEVAREKF 227

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + +   ++KM  A +  G N  +   A + +S      R   K  +KL  +LR+ +++V 
Sbjct: 228  TELRQSYEKMALAIDTHGRNHPTAELAVDELSEIFKQFRLVPKQFDKLIGSLRDSMDRVR 287

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
              E+ I+ + V+   MP+  FI +F  NE +  W+D        Y   L      ++   
Sbjct: 288  TNERLIMRMCVDNSKMPKKTFINLFAGNEASSEWIDEALNSGKPYAERLKTYEEELRRCS 347

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             KL  L+ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 348  TKLRLLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 407

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 408  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 468  KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 527

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED  +  P DAA   ++R+   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 528  FIEDTTLQLPMDAATQTNLRAATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 587

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 588  VTRERIRQIEAKALRKLRHPSRSDVLRSFLD 618



 Score =  567 bits (1461), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 306/618 (49%), Positives = 410/618 (66%), Gaps = 44/618 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVAKGKEQGYLTYAEVNDHLPEDIVDSDQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  EA   ALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DELMMTEDNADEDAIEAAAQALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I ++L   DK+  +E+++ +I               I G  +
Sbjct: 123 IEDGINQVQCSVAEYPKAISQLLDMFDKVEADELRLTDI---------------ISGFVD 167

Query: 217 NNEEKILIESSS---ADLSTEQLEKLKYESLI--------------------------KF 247
            NEE+    +++   ++LS   LE    +                             KF
Sbjct: 168 PNEEETAAPTATHIGSELSESDLEDEDRDLDEDEDEDEDGDSSDDSDDNNIDPEVAREKF 227

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           + +   ++KM  A +  G N  +   A + +S      R   K  +KL  +LR+ +++V 
Sbjct: 228 TELRQSYEKMALAIDTHGRNHPTAELAVDELSEIFKQFRLVPKQFDKLIGSLRDSMDRVR 287

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
             E+ I+ + V+   MP+  FI +F  NE +  W+D        Y   L      ++   
Sbjct: 288 TNERLIMRMCVDNSKMPKKTFINLFAGNEASSEWIDEALNSGKPYAERLKTYEEELRRCS 347

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            KL  L+ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 348 TKLRLLEEETGLSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 407

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 408 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 468 KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 527

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED  +  P DAA   ++R+   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 528 FIEDTTLQLPMDAATQTNLRAATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 587

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 588 VTRERIRQIEAKALRKLR 605


>gi|22127411|ref|NP_670834.1| RNA polymerase sigma factor RpoD [Yersinia pestis KIM10+]
 gi|21960500|gb|AAM87085.1|AE013956_10 RNA polymerase, sigma(70) factor [Yersinia pestis KIM10+]
          Length = 632

 Score =  581 bits (1497), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 314/630 (49%), Positives = 423/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 23   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 82

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 83   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 142

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 143  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 191

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 1045
                EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 192  ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 248

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 1098
              R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 249  NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 301

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
             E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 302  QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 361

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 362  KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 421

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 422  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 481

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 482  LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 541

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 542  IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 601

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 602  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 631



 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 307/617 (49%), Positives = 414/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 23  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 82

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 83  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 142

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 143 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 191

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 255
               EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 192 ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 248

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 308
             R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 249 NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 301

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
            E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 302 QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 361

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 362 KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 421

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 422 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 481

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 482 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 541

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 542 IEDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 601

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 602 TRERIRQIEAKALRKLR 618


>gi|121997892|ref|YP_001002679.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
            SL1]
 gi|121589297|gb|ABM61877.1| RNA polymerase, sigma 70 subunit, RpoD [Halorhodospira halophila SL1]
          Length = 602

 Score =  581 bits (1497), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 304/605 (50%), Positives = 422/605 (69%), Gaps = 9/605 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            ++ + + K LI  GKE+G+LT++E+ND LP+DI+D + I+ II     M I+V E   D+
Sbjct: 3    QDQQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPDQIDDIIGMINDMGINVHETAPDS 62

Query: 887  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T  +D+D  E   AAL+ VD++FGRT DP++MYMREMGSVELLTR+GEI++A
Sbjct: 63   DELLLAETTVATDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGSVELLTREGEIQLA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+GL   + A+SS P    ++++  D+  + E ++ +IV G  D+   S        
Sbjct: 123  KRIEDGLDRALAALSSYPEAARQLIMLYDRAQEGEARLTDIVAGFRDREDDSEQPPEAPA 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIK-FSNISFHFDKMRKAFEKEGYNSESYIK 1063
                      E++SA+   +       E++ + F  +   +++M++    EG  S    +
Sbjct: 183  APEAAADEDEEATSAETGPDP------EAVAELFERLRAAYNEMQEVLATEGSASPRIAE 236

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +    L I+FT K ++ + D LR  ++ +   E++I+ +   +  M R  F+K F 
Sbjct: 237  LRGELEEVFLSIKFTPKVVDAVADRLRGTVDTIRAREREIMNLCTREGRMARKEFVKSFQ 296

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
            + E +  W+D+      +    L  +  +I++ Q +L  +     L + ++++INR+M  
Sbjct: 297  DRETDPTWLDDLLAEGEERAERLQPHAEAIRKAQSELKEIADKNGLSVAEIKEINRRMSI 356

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 357  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 416

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G E  P  +A +M
Sbjct: 417  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERM 476

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            EMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED ++ +P D+A +  +R  V+++
Sbjct: 477  EMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSVTSPVDSATSEGLRESVREV 536

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L
Sbjct: 537  LSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDGL 596

Query: 1424 KIFLE 1428
            + FLE
Sbjct: 597  RSFLE 601



 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 300/600 (50%), Positives = 416/600 (69%), Gaps = 10/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           ++ + + K LI  GKE+G+LT++E+ND LP+DI+D + I+ II     M I+V E   D+
Sbjct: 3   QDQQSQIKQLIAKGKEQGFLTYAEVNDHLPDDIVDPDQIDDIIGMINDMGINVHETAPDS 62

Query: 97  ETLMLSNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T  +D+D  E   AAL+ VD++FGRT DP++MYMREMGSVELLTR+GEI++A
Sbjct: 63  DELLLAETTVATDEDEAEEAAAALAAVDAEFGRTTDPVRMYMREMGSVELLTREGEIQLA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+GL   + A+SS P    ++++  D+  + E ++ +IV G  D+   S        
Sbjct: 123 KRIEDGLDRALAALSSYPEAARQLIMLYDRAQEGEARLTDIVAGFRDREDDSEQPPEAPA 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIK-FSNISFHFDKMRKAFEKEGYNSESYIK 273
                     E++SA+   +       E++ + F  +   +++M++    EG  S    +
Sbjct: 183 APEAAADEDEEATSAETGPDP------EAVAELFERLRAAYNEMQEVLATEGSASPRIAE 236

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +    L I+FT K ++ + D LR  ++ +   E++I+ +   +  M R  F+K F 
Sbjct: 237 LRGELEEVFLSIKFTPKVVDAVADRLRGTVDTIRAREREIMNLCTREGRMARKEFVKSFQ 296

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
           + E +  W+D+      +    L  +  +I++ Q +L  +     L + ++++INR+M  
Sbjct: 297 DRETDPTWLDDLLAEGEERAERLQPHAEAIRKAQSELKEIADKNGLSVAEIKEINRRMSI 356

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 357 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 416

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G E  P  +A +M
Sbjct: 417 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERM 476

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           EMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED ++ +P D+A +  +R  V+++
Sbjct: 477 EMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSVTSPVDSATSEGLRESVREV 536

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L+ LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 537 LSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDGL 596


>gi|374336959|ref|YP_005093646.1| RNA polymerase sigma factor RpoD [Oceanimonas sp. GK1]
 gi|372986646|gb|AEY02896.1| RNA polymerase sigma factor RpoD [Oceanimonas sp. GK1]
          Length = 614

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/607 (49%), Positives = 412/607 (67%), Gaps = 11/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + LM+
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   SETTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  ++S  P  I  +L   D+    +IK+ +I+ G +D    +++         +E  
Sbjct: 128  NQVQSSVSEYPEAITSLLDQFDRFEAGDIKLSDIISGFVDLE-EADDVAPTATHIGSELS 186

Query: 1012 ILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSESY 1061
                    D   E  +  +               KF  +   ++ +R     +G  S+  
Sbjct: 187  DKDLDDEDDDEDEDEDDDEESDTDNGPDPEVAREKFGQLRTQYEAVRDTIAAKGRTSDEA 246

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +    +++     R   K  ++L +++R+ + +V   E+ I+++ V +C MP+  F++ 
Sbjct: 247  AEQITALADLFRQFRLVPKQFDRLVNSMRDMMERVRVQERIIMKLCVEQCKMPKKTFVQA 306

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  +E    W + +      ++  L      +     KL  ++ +  L ++ ++DINR+M
Sbjct: 307  FAHHESEQAWFNAQLAAGKTWSARLQDVSEDVLRAIGKLKTVEEETGLTISQIKDINRRM 366

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 367  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 426

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 427  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAH 486

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+D+A + S+R+  K
Sbjct: 487  RMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPADSATSESLRNATK 546

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 547  DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 606

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 607  VLRSFLD 613



 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/594 (49%), Positives = 403/594 (67%), Gaps = 11/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + LM+
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  SETTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  ++S  P  I  +L   D+    +IK+ +I+ G +D    +++         +E  
Sbjct: 128 NQVQSSVSEYPEAITSLLDQFDRFEAGDIKLSDIISGFVDLE-EADDVAPTATHIGSELS 186

Query: 222 ILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSESY 271
                   D   E  +  +               KF  +   ++ +R     +G  S+  
Sbjct: 187 DKDLDDEDDDEDEDEDDDEESDTDNGPDPEVAREKFGQLRTQYEAVRDTIAAKGRTSDEA 246

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +    +++     R   K  ++L +++R+ + +V   E+ I+++ V +C MP+  F++ 
Sbjct: 247 AEQITALADLFRQFRLVPKQFDRLVNSMRDMMERVRVQERIIMKLCVEQCKMPKKTFVQA 306

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  +E    W + +      ++  L      +     KL  ++ +  L ++ ++DINR+M
Sbjct: 307 FAHHESEQAWFNAQLAAGKTWSARLQDVSEDVLRAIGKLKTVEEETGLTISQIKDINRRM 366

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 367 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 426

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 427 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAH 486

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+D+A + S+R+  K
Sbjct: 487 RMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPADSATSESLRNATK 546

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|56461300|ref|YP_156581.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
            L2TR]
 gi|56180310|gb|AAV83032.1| DNA-directed RNA polymerase sigma 70 subunit [Idiomarina loihiensis
            L2TR]
          Length = 609

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 311/606 (51%), Positives = 418/606 (68%), Gaps = 4/606 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+G+LTF+E+ND LP++I+D + +E II+    M I V E   D 
Sbjct: 3    QNRQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQVEDIIRMINDMGIRVFESAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LM++   +D+D  E    AL++VD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMMAESAADEDAAEEAAQALASVDGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEG+  +  +++  P  I  +L   D     E+++ +I+ G ID +      V   N  
Sbjct: 123  IEEGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTDIISGFIDPDEVDEAPVAATNVG 182

Query: 1007 N---NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +   +EE    +    +   E    +  E +  KF+ +   ++  R+A  K G +     
Sbjct: 183  SELPSEELEKSDDDDDEDEEEADTGIDPEFARSKFNALREQYEATRQAIAKHGRDGAGAR 242

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
               + +S+     R   K  ++L   +R  + +V   E+ I++I V +  MP+ +F+K F
Sbjct: 243  VEIDKLSDLFKQFRLVPKQFDRLVKDMRAMMQRVRVQERIIMKISVEQGEMPKRNFMKAF 302

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              +E N+ WVD E      Y+  L      I+    KL++++ +  L +  +++INR+M 
Sbjct: 303  ATHENNMAWVDKEIDSGASYSDTLKEVRGEIERCVNKLVDVERETGLTIGKVKEINRRMS 362

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 363  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 422

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 423  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAER 482

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R+ V+D
Sbjct: 483  MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNSVRD 542

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +
Sbjct: 543  VLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 602

Query: 1423 LKIFLE 1428
            LK FL+
Sbjct: 603  LKSFLD 608



 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/593 (51%), Positives = 408/593 (68%), Gaps = 4/593 (0%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+G+LTF+E+ND LP++I+D + +E II+    M I V E   D 
Sbjct: 3   QNRQSQLKVLIAKGKEQGFLTFAEVNDHLPQEIVDSDQVEDIIRMINDMGIRVFESAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LM++   +D+D  E    AL++VD + GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMMAESAADEDAAEEAAQALASVDGEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEG+  +  +++  P  I  +L   D     E+++ +I+ G ID +      V   N  
Sbjct: 123 IEEGINQVQCSVAEYPEAINFLLEQWDSYEAEELRLTDIISGFIDPDEVDEAPVAATNVG 182

Query: 217 N---NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           +   +EE    +    +   E    +  E +  KF+ +   ++  R+A  K G +     
Sbjct: 183 SELPSEELEKSDDDDDEDEEEADTGIDPEFARSKFNALREQYEATRQAIAKHGRDGAGAR 242

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
              + +S+     R   K  ++L   +R  + +V   E+ I++I V +  MP+ +F+K F
Sbjct: 243 VEIDKLSDLFKQFRLVPKQFDRLVKDMRAMMQRVRVQERIIMKISVEQGEMPKRNFMKAF 302

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             +E N+ WVD E      Y+  L      I+    KL++++ +  L +  +++INR+M 
Sbjct: 303 ATHENNMAWVDKEIDSGASYSDTLKEVRGEIERCVNKLVDVERETGLTIGKVKEINRRMS 362

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 363 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 422

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 423 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAER 482

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+R+ V+D
Sbjct: 483 MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTLDLPIDSATSESLRNSVRD 542

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 VLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 595


>gi|388455429|ref|ZP_10137724.1| RNA polymerase sigma factor rpoD (sigma-70) [Fluoribacter dumoffii
            Tex-KL]
          Length = 619

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 313/606 (51%), Positives = 409/606 (67%), Gaps = 15/606 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 894
            +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 14   VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 72

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
                D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73   EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            + +++  P T+  +L   D+ +  EI+++EI+ G  D           G+  +  +   +
Sbjct: 132  LKSLAHYPETVQLVLDDYDRFNAQEIRLNEIISGFSDVEDEIAPAANIGSMLDEAQMDDL 191

Query: 1015 ESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
              S  +   E    +          ++ I F ++   +D    + ++ G      +K   
Sbjct: 192  LLSEDEEDEEGEGGIGEVDDGPNPEQAKIYFDDLRNTYDTAVVSLKEHGREHAKTLKCLE 251

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +S   L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252  AMSESFLKLKLTSRQVDRLTRHFRQLRNHIREYERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 1127 INLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             ++ W+ N    +H   L L R       I  +Q +L+  + +  L + +++DINRKM  
Sbjct: 312  TDMEWL-NGIIAKHGKKLDLNRIQEYTEEILRIQSRLVAFEIEYGLTIAEIKDINRKMSI 370

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A KM
Sbjct: 431  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKM 490

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            E+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +I
Sbjct: 491  ELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEI 550

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KL
Sbjct: 551  LETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKL 610

Query: 1424 KIFLEG 1429
            + FLEG
Sbjct: 611  RSFLEG 616



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 303/592 (51%), Positives = 398/592 (67%), Gaps = 15/592 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE-HVLDTETLMLSNI 104
           +I LGKE+GYLT+S+IND LP +I+D E  + II     M+I V E    D E  +L N 
Sbjct: 14  VISLGKEQGYLTYSQINDLLP-NIVDTEHFDVIISMLEGMNIKVFELPPGDDELALLLNT 72

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
               D+EEA    L++VD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+  +
Sbjct: 73  EEVPDIEEAA-MVLASVDKETGRTTDPVRMYMREMGTVELLTREGEIRIAKRIEEGIYQV 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           + +++  P T+  +L   D+ +  EI+++EI+ G  D           G+  +  +   +
Sbjct: 132 LKSLAHYPETVQLVLDDYDRFNAQEIRLNEIISGFSDVEDEIAPAANIGSMLDEAQMDDL 191

Query: 225 ESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
             S  +   E    +          ++ I F ++   +D    + ++ G      +K   
Sbjct: 192 LLSEDEEDEEGEGGIGEVDDGPNPEQAKIYFDDLRNTYDTAVVSLKEHGREHAKTLKCLE 251

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +S   L ++ T++ +++L    R   N + + E+ I+ + + K  +PR  FI  FP  E
Sbjct: 252 AMSESFLKLKLTSRQVDRLTRHFRQLRNHIREYERSIMRLCIEKARIPRKLFIDTFPGQE 311

Query: 337 INLNWVDNETKIQHDYNLILCR---NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            ++ W+ N    +H   L L R       I  +Q +L+  + +  L + +++DINRKM  
Sbjct: 312 TDMEWL-NGIIAKHGKKLDLNRIQEYTEEILRIQSRLVAFEIEYGLTIAEIKDINRKMSI 370

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  +A KM
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGREATPEELAEKM 490

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           E+ E+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED N+ +P D A    +R    +I
Sbjct: 491 ELSEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDNNIESPIDMATAEGLREATLEI 550

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L +LTPRE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 LETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|238750950|ref|ZP_04612447.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
 gi|238710864|gb|EEQ03085.1| RNA polymerase sigma factor rpoD [Yersinia rohdei ATCC 43380]
          Length = 612

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 311/617 (50%), Positives = 418/617 (67%), Gaps = 23/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E          D   ++ E+    S+       KFS +   ++  R   +K G   
Sbjct: 182  HVGSELSTEEMDDDDDEEEDEEEEEDDNSIDPELARQKFSELREQYESTRMEIKKNG--- 238

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239  ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295  KMPKKNFVTLFSSNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 595  RKLRHPSRSEVLRSFLD 611



 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/604 (50%), Positives = 409/604 (67%), Gaps = 23/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEEGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E          D   ++ E+    S+       KFS +   ++  R   +K G   
Sbjct: 182 HVGSELSTEEMDDDDDEEEDEEEEEDDNSIDPELARQKFSELREQYESTRMEIKKNG--- 238

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239 ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295 KMPKKNFVTLFSSNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 622 RKLR 625
           RKLR
Sbjct: 595 RKLR 598


>gi|1710688|sp|P52327.1|RPOD_PSEPU RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|762877|dbj|BAA06281.1| principal sigma factor [Pseudomonas putida]
 gi|1586519|prf||2204230A sigma factor
          Length = 614

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 419/607 (69%), Gaps = 13/607 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+ V++D  RT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAVETDIRRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
            ++++ AI+  P T+  IL   D++++   ++ +++ G ID +      +    I G K  
Sbjct: 130  REVMGAIAHFPGTVDYILGEYDRVNRG-CRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 188

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH------FDKMRKAFEKEGYNSESY 1061
              ++   +        +  E+ K  +L + S  S        F   +   EK  Y  +  
Sbjct: 189  AAKEEADDDEEESEGGDDEEEPKA-ALTRSSQPSVSVRYPSSFSDHQGPEEKRSY-PQGK 246

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++
Sbjct: 247  RRALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRM 306

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M
Sbjct: 307  FPSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRM 366

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 367  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 426

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 427  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 486

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P   A   S++   +
Sbjct: 487  RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIYVATVESLKEATR 546

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA RKLRHP+R  
Sbjct: 547  DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAWRKLRHPTRSE 606

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 607  HLRSFLD 613



 Score =  567 bits (1461), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 306/594 (51%), Positives = 410/594 (69%), Gaps = 13/594 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RIKELITRGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFESAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+ V++D  RT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAVETDIRRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
           ++++ AI+  P T+  IL   D++++   ++ +++ G ID +      +    I G K  
Sbjct: 130 REVMGAIAHFPGTVDYILGEYDRVNRG-CRLSDVLSGYIDPDDNIAAPTEEVPIPGTKAA 188

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH------FDKMRKAFEKEGYNSESY 271
             ++   +        +  E+ K  +L + S  S        F   +   EK  Y  +  
Sbjct: 189 AAKEEADDDEEESEGGDDEEEPKA-ALTRSSQPSVSVRYPSSFSDHQGPEEKRSY-PQGK 246

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +A   +++  + I+   K  E L + +R+ +N++ Q E+ I+++ V    MPR  F+++
Sbjct: 247 RRALQALADLFMPIKLVPKQFEVLVERVRDALNRLRQQERAIMQLCVRDARMPRADFLRM 306

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP NE +  W  +  K    +   L     +I   QQKLI+L+T+  L + ++++INR+M
Sbjct: 307 FPSNETDQTWSGDLAKRNTKWAAALGEKDAAIVACQQKLIDLETETGLTVAEIKEINRRM 366

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 367 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 426

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 427 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 486

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P   A   S++   +
Sbjct: 487 RMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIYVATVESLKEATR 546

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA RKLR
Sbjct: 547 DVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAWRKLR 600


>gi|387887870|ref|YP_006318168.1| RNA polymerase [Escherichia blattae DSM 4481]
 gi|414594822|ref|ZP_11444455.1| RNA polymerase sigma-D factor [Escherichia blattae NBRC 105725]
 gi|386922703|gb|AFJ45657.1| RNA polymerase [Escherichia blattae DSM 4481]
 gi|403194127|dbj|GAB82107.1| RNA polymerase sigma-D factor [Escherichia blattae NBRC 105725]
          Length = 614

 Score =  580 bits (1496), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 414/611 (67%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML      +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLGENTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEETRLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
              +   +  ++    +      +    ++ I        F ++R  +E      ++  ++
Sbjct: 183  VGSELSQEDMDDDEDEDDDSDDDSSDDDNSIDPELAREKFAELRAQYEVTRDTIKAKGRS 242

Query: 1065 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            H     E+L +       R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAAIAMNKPWSEKLRDVTEDVQRCLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 405/598 (67%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML      +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLGENTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEETRLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
             +   +  ++    +      +    ++ I        F ++R  +E      ++  ++
Sbjct: 183 VGSELSQEDMDDDEDEDDDSDDDSSDDDNSIDPELAREKFAELRAQYEVTRDTIKAKGRS 242

Query: 275 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           H     E+L +       R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRSMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAAIAMNKPWSEKLRDVTEDVQRCLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|292490206|ref|YP_003525645.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
 gi|291578801|gb|ADE13258.1| RNA polymerase sigma factor RpoD [Nitrosococcus halophilus Nc4]
          Length = 602

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/609 (49%), Positives = 423/609 (69%), Gaps = 20/609 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            ++ + + K+LI  GK+RGYL++SE+ND LP+D+ID E IE II  F  M ISV E + + 
Sbjct: 3    QDRQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEA 62

Query: 887  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + L ++    +DD+  E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 63   DALAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEIRIAK 122

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------KNFSSNNR 999
            RIEEG++ +  A+S  P ++ E+L   +++   + ++ +++ G  +      K   +   
Sbjct: 123  RIEEGMRQVHTALSLFPGSVAELLRQYERVEAGDARLADMISGFHEPEEEDIKEAVAEEE 182

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
             +  +  ++EE+        + + EQ  +L+   L +    +   D  +   E     SE
Sbjct: 183  AVADSAEDSEEEENGGGPDPERAREQFVQLR--ELYRLRQEAASKDDGKALAELSEAMSE 240

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
             +++            +   +   +L + LR  +  +  +E+ I++I VN+  MPR  F+
Sbjct: 241  CFLR-----------FKLVPRLSLQLIEGLRAVVAGIRVLERTIMQIAVNEAHMPRQDFL 289

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
              F   E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + + ++++ NR
Sbjct: 290  SSFQGQETNLNWVEKHIRAKKHYSSVLRKKGEAIRQAQEKLIALEQGAGMSVAEIKEANR 349

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
             +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 350  SLSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 409

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +
Sbjct: 410  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDEL 469

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +++MP++K+RK++KIAKEP+SME+P+GDDEDSHLGDF+ED  +++P DAA+ + +R  
Sbjct: 470  AERVDMPKDKVRKVLKIAKEPISMETPIGDDEDSHLGDFVEDAEVVSPPDAAIFSGLRET 529

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
             + IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 530  TQQILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 589

Query: 1420 YYKLKIFLE 1428
              +L+ FL+
Sbjct: 590  SEQLRSFLD 598



 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/596 (49%), Positives = 413/596 (69%), Gaps = 20/596 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           ++ + + K+LI  GK+RGYL++SE+ND LP+D+ID E IE II  F  M ISV E + + 
Sbjct: 3   QDRQSQLKLLIARGKDRGYLSYSEVNDHLPDDVIDPEQIEDIITMFNDMGISVHEDMAEA 62

Query: 97  ETL-MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + L ++    +DD+  E   AAL +VD +F RT DP++MYMREMGSVELLTR+GEI IAK
Sbjct: 63  DALAIMDTAVADDEAAEEAAAALVSVDGEFARTSDPVRMYMREMGSVELLTREGEIRIAK 122

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------KNFSSNNR 209
           RIEEG++ +  A+S  P ++ E+L   +++   + ++ +++ G  +      K   +   
Sbjct: 123 RIEEGMRQVHTALSLFPGSVAELLRQYERVEAGDARLADMISGFHEPEEEDIKEAVAEEE 182

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
            +  +  ++EE+        + + EQ  +L+   L +    +   D  +   E     SE
Sbjct: 183 AVADSAEDSEEEENGGGPDPERAREQFVQLR--ELYRLRQEAASKDDGKALAELSEAMSE 240

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
            +++            +   +   +L + LR  +  +  +E+ I++I VN+  MPR  F+
Sbjct: 241 CFLR-----------FKLVPRLSLQLIEGLRAVVAGIRVLERTIMQIAVNEAHMPRQDFL 289

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
             F   E NLNWV+   + +  Y+ +L +   +I++ Q+KLI L+    + + ++++ NR
Sbjct: 290 SSFQGQETNLNWVEKHIRAKKHYSSVLRKKGEAIRQAQEKLIALEQGAGMSVAEIKEANR 349

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
            +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 350 SLSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 409

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +
Sbjct: 410 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPDEL 469

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +++MP++K+RK++KIAKEP+SME+P+GDDEDSHLGDF+ED  +++P DAA+ + +R  
Sbjct: 470 AERVDMPKDKVRKVLKIAKEPISMETPIGDDEDSHLGDFVEDAEVVSPPDAAIFSGLRET 529

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            + IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 530 TQQILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 585


>gi|300718455|ref|YP_003743258.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
            Eb661]
 gi|299064291|emb|CAX61411.1| Sigma D (Sigma 70) factor of RNA polymerase [Erwinia billingiae
            Eb661]
          Length = 612

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 413/609 (67%), Gaps = 7/609 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 1000
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDMITGFVDPNAEAEIAPTATH 182

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 1059
            +    +  E     E    +   E    +  E +  KF+++   ++K R   + +G +  
Sbjct: 183  VGSELSEAERNDNDEEEEDEDDAEDDNSIDPELAREKFNDLRVQYEKARTVIKAKGRSHA 242

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
                   N+S+     R   K  + L +++R  +++V   E+ I++  V  C MP+ +FI
Sbjct: 243  DAAAEIQNLSDVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERLIMKFCVEICKMPKKNFI 302

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
             +F  NE +  W      +   ++  L      ++    KL  ++ +  L +  ++DINR
Sbjct: 303  TLFTGNETSETWFKAALAMNKPWSEKLKDVADDVQRGLMKLGQIEQETGLTIEQVKDINR 362

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
            +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363  RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483  AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 543  THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 602

Query: 1420 YYKLKIFLE 1428
               L+ FL+
Sbjct: 603  SEVLRSFLD 611



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 299/596 (50%), Positives = 404/596 (67%), Gaps = 7/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRV 210
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N     +     
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDMITGFVDPNAEAEIAPTATH 182

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSE 269
           +    +  E     E    +   E    +  E +  KF+++   ++K R   + +G +  
Sbjct: 183 VGSELSEAERNDNDEEEEDEDDAEDDNSIDPELAREKFNDLRVQYEKARTVIKAKGRSHA 242

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
                  N+S+     R   K  + L +++R  +++V   E+ I++  V  C MP+ +FI
Sbjct: 243 DAAAEIQNLSDVFKQFRLVPKQFDFLVNSMRIMMDRVRTQERLIMKFCVEICKMPKKNFI 302

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
            +F  NE +  W      +   ++  L      ++    KL  ++ +  L +  ++DINR
Sbjct: 303 TLFTGNETSETWFKAALAMNKPWSEKLKDVADDVQRGLMKLGQIEQETGLTIEQVKDINR 362

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
           +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 363 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 422

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +
Sbjct: 423 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 482

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS 
Sbjct: 483 AERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSA 542

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 THDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|333909193|ref|YP_004482779.1| RNA polymerase sigma-70 subunit RpoD [Marinomonas posidonica
            IVIA-Po-181]
 gi|333479199|gb|AEF55860.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas posidonica
            IVIA-Po-181]
          Length = 613

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/614 (50%), Positives = 412/614 (67%), Gaps = 26/614 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLTF+E+ND LP+D+ D E +E II     M I+VSE+  D E+L++
Sbjct: 8    RLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEYAPDKESLLM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
                T+D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68   EEGDTTDEAAAEEAAAALAAVEGDITRTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++++ AIS  P  +  +L A  K+ + E ++ +I  G ID +         G +   EE
Sbjct: 128  TREVMAAISYFPGAVDVLLNAYAKVQEEEGRLSDIFSGFIDGD---------GEEPVFEE 178

Query: 1011 ---KILIESSSADLSTEQLEKLKY-------------ESLIKFSNISFHFDKMRKAFEKE 1054
               ++ IE  + D  +   E                 E+ ++F+ I+  + +++   E  
Sbjct: 179  LAEELPIEEEADDSDSNDEEDDSESSEEETDNGPDPEETALRFNEIARIYGELKVLLETR 238

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
                         +S     I+   K  ++L D +R+++ +V + E+ I+++ V K GMP
Sbjct: 239  NRQDSVVKSKQEELSISFAPIKLVPKLFDELIDRVRSRMEKVREQERLIMQVCVRKSGMP 298

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            R  F+K FP NE N +W+  +     +Y+  L  N       Q+KL  +  +  L + +L
Sbjct: 299  RTEFLKRFPSNETNPDWLQEQIAASANYSAALEENEAEFMRSQRKLRAVSKETGLTIAEL 358

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            ++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 359  KEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 419  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 478

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A   
Sbjct: 479  TPEELAARMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIE 538

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
             +R     +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 539  GLRESTTTVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 599  RHPSRSEHLRSFLD 612



 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/601 (50%), Positives = 403/601 (67%), Gaps = 26/601 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLTF+E+ND LP+D+ D E +E II     M I+VSE+  D E+L++
Sbjct: 8   RLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEYAPDKESLLM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
               T+D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68  EEGDTTDEAAAEEAAAALAAVEGDITRTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++++ AIS  P  +  +L A  K+ + E ++ +I  G ID +         G +   EE
Sbjct: 128 TREVMAAISYFPGAVDVLLNAYAKVQEEEGRLSDIFSGFIDGD---------GEEPVFEE 178

Query: 221 ---KILIESSSADLSTEQLEKLKY-------------ESLIKFSNISFHFDKMRKAFEKE 264
              ++ IE  + D  +   E                 E+ ++F+ I+  + +++   E  
Sbjct: 179 LAEELPIEEEADDSDSNDEEDDSESSEEETDNGPDPEETALRFNEIARIYGELKVLLETR 238

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
                        +S     I+   K  ++L D +R+++ +V + E+ I+++ V K GMP
Sbjct: 239 NRQDSVVKSKQEELSISFAPIKLVPKLFDELIDRVRSRMEKVREQERLIMQVCVRKSGMP 298

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           R  F+K FP NE N +W+  +     +Y+  L  N       Q+KL  +  +  L + +L
Sbjct: 299 RTEFLKRFPSNETNPDWLQEQIAASANYSAALEENEAEFMRSQRKLRAVSKETGLTIAEL 358

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           ++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 359 KEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 478

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A   
Sbjct: 479 TPEELAARMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIE 538

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
            +R     +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 539 GLRESTTTVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598

Query: 625 R 625
           R
Sbjct: 599 R 599


>gi|398799724|ref|ZP_10559006.1| RNA polymerase sigma factor, sigma-70 family [Pantoea sp. GM01]
 gi|398097726|gb|EJL88029.1| RNA polymerase sigma factor, sigma-70 family [Pantoea sp. GM01]
          Length = 613

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 409/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G ID N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGDSRLSDLIIGFIDPNAEEDIAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 1058
              +   +   +    +   +        S+       KF ++   ++  R   + +G + 
Sbjct: 183  VGSELSQEDRDDDEEEDEEDDDSSDDDNSIDPELAREKFGDLRTQYETTRTVIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               +    N+S      R   K  + L + +R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243  ADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE N +W      +   ++  L      +     KL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETNPSWFKAALAMNKPWSEKLLEVEDDVNRSLYKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 400/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  +SD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLILNENSSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G ID N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGDSRLSDLIIGFIDPNAEEDIAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI------KFSNISFHFDKMRKAFEKEGYNS 268
             +   +   +    +   +        S+       KF ++   ++  R   + +G + 
Sbjct: 183 VGSELSQEDRDDDEEEDEEDDDSSDDDNSIDPELAREKFGDLRTQYETTRTVIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              +    N+S      R   K  + L + +R  + +V   E+ I+++ +  C MP+ +F
Sbjct: 243 ADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERLIMKLCIELCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE N +W      +   ++  L      +     KL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETNPSWFKAALAMNKPWSEKLLEVEDDVNRSLYKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRS 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|359449143|ref|ZP_09238642.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20480]
 gi|358045054|dbj|GAA74891.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20480]
          Length = 613

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 321/619 (51%), Positives = 414/619 (66%), Gaps = 33/619 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +E  
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDEAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY--------------------ESLIKFSNISFHFDKMRKAF 1051
            I   +  ++LS +QL+                        E+ I F N+   ++K R  F
Sbjct: 175  ISATNIGSELSEKQLDDDDEDDDKSDDDEDEEVDTGPDPEEARIHFENLRDLYNKARDTF 234

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            E +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V   
Sbjct: 235  EAKGRSHPDSQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQIA 294

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L +
Sbjct: 295  KLPKKAFVKHFANNETDPSWVDLEISNNEKYSAKLEEVKPEIIRCINKLSIIEQTTGLSI 354

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355  ERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A
Sbjct: 475  REPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSA 534

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535  TMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 1412 RKLRHPSRYYKLKIFLEGK 1430
            RKLRHPSR   LK FL+ K
Sbjct: 595  RKLRHPSRSDLLKSFLDAK 613



 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 315/612 (51%), Positives = 407/612 (66%), Gaps = 34/612 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +E  
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDEAP 174

Query: 222 ILIESSSADLSTEQLEKLKY--------------------ESLIKFSNISFHFDKMRKAF 261
           I   +  ++LS +QL+                        E+ I F N+   ++K R  F
Sbjct: 175 ISATNIGSELSEKQLDDDDEDDDKSDDDEDEEVDTGPDPEEARIHFENLRDLYNKARDTF 234

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           E +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V   
Sbjct: 235 EAKGRSHPDSQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQIA 294

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L +
Sbjct: 295 KLPKKAFVKHFANNETDPSWVDLEISNNEKYSAKLEEVKPEIIRCINKLSIIEQTTGLSI 354

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355 ERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A
Sbjct: 475 REPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSA 534

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535 TMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 622 RKLR-PLAHDWL 632
           RKLR P   D L
Sbjct: 595 RKLRHPSRSDLL 606


>gi|359786793|ref|ZP_09289881.1| RNA polymerase sigma factor RpoD [Halomonas sp. GFAJ-1]
 gi|359295900|gb|EHK60157.1| RNA polymerase sigma factor RpoD [Halomonas sp. GFAJ-1]
          Length = 616

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 314/607 (51%), Positives = 405/607 (66%), Gaps = 11/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   SDHSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130  REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 1062
            E  + +    D   E  +    E           F+++R+       AF K G  S    
Sbjct: 190  EPEIDDDVDNDGDDEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKYGRGSAELK 249

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250  AEQTRLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 1181
            P +E +  W+D   + Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310  PGSESDPKWLDAFQEAQPKYADRLEPLRADIARSQRK-IAFEEDMVQLTVADLKEVNRKL 368

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489  RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 549  NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 608

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 609  PLRSFLD 615



 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 307/594 (51%), Positives = 396/594 (66%), Gaps = 11/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV+E   D +TLM+
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVAEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  SDHSTDESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ +++  P  +  IL A D     E   ++ ++  G ID +                
Sbjct: 130 REVMSSLAYLPGAVASILDAYDATQDEEAPGRLSDLFSGFIDPDEGIPGVAEAEVPEPEP 189

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK-------AFEKEGYNSESYI 272
           E  + +    D   E  +    E           F+++R+       AF K G  S    
Sbjct: 190 EPEIDDDVDNDGDDEDEDSTASEGGPDPEEARARFEQIREQNALVEAAFAKYGRGSAELK 249

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                ++     I+   K  E+L   +R  + QV   EK ++++ V K  +PR  FIK F
Sbjct: 250 AEQTRLAVLFSPIKLVPKHFERLVGQVRISVEQVRAQEKAVMQLCVKKAKVPRKTFIKSF 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV-LPLNDLRDINRKM 391
           P +E +  W+D   + Q  Y   L      I   Q+K I  + D+V L + DL+++NRK+
Sbjct: 310 PGSESDPKWLDAFQEAQPKYADRLEPLRADIARSQRK-IAFEEDMVQLTVADLKEVNRKL 368

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 369 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 428

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +  
Sbjct: 429 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELGE 488

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D A    +    +
Sbjct: 489 RLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDMATGEGLIEATR 548

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 NVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|162420372|ref|YP_001604920.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
 gi|162353187|gb|ABX87135.1| RNA polymerase sigma factor RpoD [Yersinia pestis Angola]
          Length = 612

 Score =  580 bits (1495), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 313/630 (49%), Positives = 423/630 (67%), Gaps = 49/630 (7%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 1045
                EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 172  ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 228

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 1098
              R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229  NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 281

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
             E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 282  QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 341

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342  KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462  LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A + ++RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522  IEDTTLELPLDSATSENLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 582  TRERIRQIEAKALRKLRHPSRSEVLRSFLD 611



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 306/617 (49%), Positives = 414/617 (67%), Gaps = 49/617 (7%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLI-----------------KFSNISFHFD 255
               EE I   ++   ++LSTE+++    +                    KFS++   ++
Sbjct: 172 ---AEEDIAPTATHVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYE 228

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQ 308
             R   +K G N       H N + E+L +       R   K  + L + +R  +++V  
Sbjct: 229 NARMEIKKNGRN-------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRT 281

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
            E+ I+++ V +C MP+ +F+ +F  NE +  W +    +   ++  L      ++   Q
Sbjct: 282 QERIIMKLCVEQCKMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQ 341

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           KL  ++ +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 342 KLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 401

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 402 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 461

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDF
Sbjct: 462 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 521

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A + ++RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 522 IEDTTLELPLDSATSENLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 582 TRERIRQIEAKALRKLR 598


>gi|218550316|ref|YP_002384107.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ATCC 35469]
 gi|424817600|ref|ZP_18242751.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ECD227]
 gi|218357857|emb|CAQ90501.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia fergusonii
            ATCC 35469]
 gi|325498620|gb|EGC96479.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ECD227]
          Length = 613

 Score =  580 bits (1494), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYEVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   ++  R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYEVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVADEVHRSLQKLHQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|392952342|ref|ZP_10317897.1| RNA polymerase sigma factor [Hydrocarboniphaga effusa AP103]
 gi|391861304|gb|EIT71832.1| RNA polymerase sigma factor [Hydrocarboniphaga effusa AP103]
          Length = 616

 Score =  580 bits (1494), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/632 (48%), Positives = 424/632 (67%), Gaps = 41/632 (6%)

Query: 820  SNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 879
            SNS E+    + + K+LI LGKE+GYLT++E++D LPE ++D E I+ +I   + M I V
Sbjct: 2    SNSAEK----QSQIKVLIALGKEKGYLTYAEVSDHLPE-VVDSEQIDDVISMIQTMGIQV 56

Query: 880  SEHVLDTETLMLSN------ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVE 933
             +   D E+ + S          ++D  E   AAL+  D  FGRT DP++MYMREMGSVE
Sbjct: 57   HDEAPDEESQLFSEPAVVASAEEEEDAAEEAAAALAASDDQFGRTTDPVRMYMREMGSVE 116

Query: 934  LLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN 993
            LL R+GEI IAKRIEEGL + ++A++  P T+  +L A   + + + ++ E++ G  D N
Sbjct: 117  LLDREGEIRIAKRIEEGLNEALYAMAIYPETVKILLDAYASVGEGKRRLAEVITGFFDPN 176

Query: 994  FSSNNRVIK-------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNI 1040
                                   N   +EE+  +++               E+ +KF  +
Sbjct: 177  AEPVAEAPPPPVEEEEEEEEEDDNAGGDEEEEAVDTGPD----------PEEARLKFEEL 226

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
               +D   KA +K G + +  +     +++ ++  + + K ++++   LRN+I  + +IE
Sbjct: 227  QSLYDTAWKALQKTGADDKKTLGKREAVADLIMTFKLSPKIVDEINRNLRNKIENIREIE 286

Query: 1101 KQILEIVVNKCGMPRLHFIKVF----PENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
            + ++ I V   GM R  F+  +    P++    +W++   + +  Y+  L      I EL
Sbjct: 287  RSVMRICVIDAGMSREEFLGKYKGTKPDDH---DWLEKSIRAKRKYSATLATRHDEIVEL 343

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
              +L  ++ + ++ +++++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 344  LGQLTKIENEFLIAVDEIKDINRRMNVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 403

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 404  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 463

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ+LQE G EP P  +A+KMEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 464  NKLNRISRQMLQEMGREPTPEELAVKMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 523

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED   ++P ++A ++S+      IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 524  DFIEDTAAVSPLESATSSSLAEATHQILASLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 583

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 584  DVTRERIRQIEAKALRKLRHPSRANYLRSFLD 615



 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 301/619 (48%), Positives = 415/619 (67%), Gaps = 41/619 (6%)

Query: 30  SNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 89
           SNS E+    + + K+LI LGKE+GYLT++E++D LPE ++D E I+ +I   + M I V
Sbjct: 2   SNSAEK----QSQIKVLIALGKEKGYLTYAEVSDHLPE-VVDSEQIDDVISMIQTMGIQV 56

Query: 90  SEHVLDTETLMLSN------ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVE 143
            +   D E+ + S          ++D  E   AAL+  D  FGRT DP++MYMREMGSVE
Sbjct: 57  HDEAPDEESQLFSEPAVVASAEEEEDAAEEAAAALAASDDQFGRTTDPVRMYMREMGSVE 116

Query: 144 LLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN 203
           LL R+GEI IAKRIEEGL + ++A++  P T+  +L A   + + + ++ E++ G  D N
Sbjct: 117 LLDREGEIRIAKRIEEGLNEALYAMAIYPETVKILLDAYASVGEGKRRLAEVITGFFDPN 176

Query: 204 FSSNNRVIK-------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNI 250
                                  N   +EE+  +++               E+ +KF  +
Sbjct: 177 AEPVAEAPPPPVEEEEEEEEEDDNAGGDEEEEAVDTGPD----------PEEARLKFEEL 226

Query: 251 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
              +D   KA +K G + +  +     +++ ++  + + K ++++   LRN+I  + +IE
Sbjct: 227 QSLYDTAWKALQKTGADDKKTLGKREAVADLIMTFKLSPKIVDEINRNLRNKIENIREIE 286

Query: 311 KQILEIVVNKCGMPRLHFIKVF----PENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
           + ++ I V   GM R  F+  +    P++    +W++   + +  Y+  L      I EL
Sbjct: 287 RSVMRICVIDAGMSREEFLGKYKGTKPDDH---DWLEKSIRAKRKYSATLATRHDEIVEL 343

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
             +L  ++ + ++ +++++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 344 LGQLTKIENEFLIAVDEIKDINRRMNVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 403

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 404 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 463

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ+LQE G EP P  +A+KMEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 464 NKLNRISRQMLQEMGREPTPEELAVKMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 523

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED   ++P ++A ++S+      IL SLTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 524 DFIEDTAAVSPLESATSSSLAEATHQILASLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 583

Query: 607 DVTRERIRQIEAKALRKLR 625
           DVTRERIRQIEAKALRKLR
Sbjct: 584 DVTRERIRQIEAKALRKLR 602


>gi|119473196|ref|ZP_01614893.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
            bacterium TW-7]
 gi|392538022|ref|ZP_10285159.1| RNA polymerase sigma factor [Pseudoalteromonas marina mano4]
 gi|119444560|gb|EAW25875.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
            bacterium TW-7]
          Length = 614

 Score =  580 bits (1494), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 321/620 (51%), Positives = 414/620 (66%), Gaps = 34/620 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +E  
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDEAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY---------------------ESLIKFSNISFHFDKMRKA 1050
            I   +  ++LS +QL+                         E+ I F N+   ++K R  
Sbjct: 175  ISATNIGSELSEKQLDDDDEDDDKSDDDEDEEEVDTGPDPEEARIHFENLRDLYNKARDT 234

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V  
Sbjct: 235  FEAKGRSHPDSQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQI 294

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L 
Sbjct: 295  AKLPKKAFVKHFANNETDPSWVDLEISNNEKYSAKLEEVKPEIIRCINKLSIIEQTTGLS 354

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 355  IERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 414

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 415  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 474

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+
Sbjct: 475  GREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDS 534

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 535  ATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 594

Query: 1411 LRKLRHPSRYYKLKIFLEGK 1430
            LRKLRHPSR   LK FL+ K
Sbjct: 595  LRKLRHPSRSDLLKSFLDAK 614



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 315/613 (51%), Positives = 407/613 (66%), Gaps = 35/613 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +E  
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDEAP 174

Query: 222 ILIESSSADLSTEQLEKLKY---------------------ESLIKFSNISFHFDKMRKA 260
           I   +  ++LS +QL+                         E+ I F N+   ++K R  
Sbjct: 175 ISATNIGSELSEKQLDDDDEDDDKSDDDEDEEEVDTGPDPEEARIHFENLRDLYNKARDT 234

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V  
Sbjct: 235 FEAKGRSHPDSQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQI 294

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L 
Sbjct: 295 AKLPKKAFVKHFANNETDPSWVDLEISNNEKYSAKLEEVKPEIIRCINKLSIIEQTTGLS 354

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 355 IERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 414

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 415 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 474

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+
Sbjct: 475 GREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDS 534

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 535 ATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 594

Query: 621 LRKLR-PLAHDWL 632
           LRKLR P   D L
Sbjct: 595 LRKLRHPSRSDLL 607


>gi|261855081|ref|YP_003262364.1| RNA polymerase sigma-70 subunit RpoD [Halothiobacillus neapolitanus
            c2]
 gi|261835550|gb|ACX95317.1| RNA polymerase, sigma 70 subunit, RpoD [Halothiobacillus neapolitanus
            c2]
          Length = 608

 Score =  580 bits (1494), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 311/615 (50%), Positives = 422/615 (68%), Gaps = 26/615 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ +   K LI  G+E+GYLT++EI+D LPE ++D + IE II   + M ISVSE   D 
Sbjct: 3    EDQQASIKSLIARGREQGYLTYAEISDHLPEALVDADQIEDIIGMIQEMGISVSEVAPDG 62

Query: 887  ETLML---SNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            + L L   S   SD+D  EEA     S VD++FGRT DP++MYMREMG+V+LL R GEIE
Sbjct: 63   DDLGLADESRAASDEDATEEAVAVLASQVDAEFGRTTDPVRMYMREMGTVDLLNRQGEIE 122

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEGL D+  A++  P TI  +L    +I   ++++ +++ G+I+           
Sbjct: 123  IAKRIEEGLIDVTRALAFYPPTIETLLEHYARIEAGDLRMQDVIVGIIEPEVEI------ 176

Query: 1003 GNKNNNEEKIL--IESSSADLSTEQLEKLKYESLIKFSN-------ISFHFDKMRKAFEK 1053
                + EEK L   E  +++   E  ++          +       +  H  ++++  E 
Sbjct: 177  --PEDAEEKPLDVAEGKASNTDDEDEDEEDDTEEEAVVDNTLDPELVRTHLMEIKRLAEN 234

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
                S  Y+    +++++++ ++      EKL + +R  I ++  +EKQI+   V+K G+
Sbjct: 235  LDERSPEYLA---SLADQLVQLKLNPAFNEKLLEQIRQAIARIRLLEKQIMHQAVDKGGL 291

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
             R  FI+ F  NE ++ WV   TK +        +  P I+ LQ++L  +  D  L +  
Sbjct: 292  KRETFIEAFRSNESDIGWVKVATKGKPTAKFSQVQ--PEIERLQKRLNTVARDSKLTVAQ 349

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
             R+++R +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 350  TREVHRLITLGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 409

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 410  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 469

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
              P  +A +M++PE+KIRK++KIAKEP+SME+P+G+D+DS+LGDFIED++ ++P D+A N
Sbjct: 470  ATPEELAERMDLPEDKIRKVLKIAKEPISMETPIGEDDDSNLGDFIEDQSAISPMDSATN 529

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
            AS+  +V++IL SLTPRE+KVL MRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 530  ASLSEIVREILASLTPREAKVLMMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 589

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR  +L+ F+E
Sbjct: 590  LRHPSRSERLRSFIE 604



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 304/602 (50%), Positives = 412/602 (68%), Gaps = 26/602 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ +   K LI  G+E+GYLT++EI+D LPE ++D + IE II   + M ISVSE   D 
Sbjct: 3   EDQQASIKSLIARGREQGYLTYAEISDHLPEALVDADQIEDIIGMIQEMGISVSEVAPDG 62

Query: 97  ETLML---SNITSDDDV-EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           + L L   S   SD+D  EEA     S VD++FGRT DP++MYMREMG+V+LL R GEIE
Sbjct: 63  DDLGLADESRAASDEDATEEAVAVLASQVDAEFGRTTDPVRMYMREMGTVDLLNRQGEIE 122

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEGL D+  A++  P TI  +L    +I   ++++ +++ G+I+           
Sbjct: 123 IAKRIEEGLIDVTRALAFYPPTIETLLEHYARIEAGDLRMQDVIVGIIEPEVEI------ 176

Query: 213 GNKNNNEEKIL--IESSSADLSTEQLEKLKYESLIKFSN-------ISFHFDKMRKAFEK 263
               + EEK L   E  +++   E  ++          +       +  H  ++++  E 
Sbjct: 177 --PEDAEEKPLDVAEGKASNTDDEDEDEEDDTEEEAVVDNTLDPELVRTHLMEIKRLAEN 234

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
               S  Y+    +++++++ ++      EKL + +R  I ++  +EKQI+   V+K G+
Sbjct: 235 LDERSPEYLA---SLADQLVQLKLNPAFNEKLLEQIRQAIARIRLLEKQIMHQAVDKGGL 291

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
            R  FI+ F  NE ++ WV   TK +        +  P I+ LQ++L  +  D  L +  
Sbjct: 292 KRETFIEAFRSNESDIGWVKVATKGKPTAKFSQVQ--PEIERLQKRLNTVARDSKLTVAQ 349

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
            R+++R +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 350 TREVHRLITLGEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 409

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 410 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 469

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
             P  +A +M++PE+KIRK++KIAKEP+SME+P+G+D+DS+LGDFIED++ ++P D+A N
Sbjct: 470 ATPEELAERMDLPEDKIRKVLKIAKEPISMETPIGEDDDSNLGDFIEDQSAISPMDSATN 529

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
           AS+  +V++IL SLTPRE+KVL MRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 530 ASLSEIVREILASLTPREAKVLMMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 589

Query: 624 LR 625
           LR
Sbjct: 590 LR 591


>gi|88858406|ref|ZP_01133048.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
            tunicata D2]
 gi|88820023|gb|EAR29836.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
            tunicata D2]
          Length = 615

 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 320/626 (51%), Positives = 419/626 (66%), Gaps = 45/626 (7%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V E   D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVCESAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TVD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVDKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    EI++ +I+ G  D               ++EE+
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKYEAEEIRLSDIISGFFD---------------SDEEQ 172

Query: 1012 ILIESS--SADLSTEQLE-------------------------KLKYESLIKFSNISFHF 1044
              I ++   +DL+ EQL+                         +L  E+  K  ++   +
Sbjct: 173  FPIAATHIGSDLNDEQLKDEDVDLDDDDDDDSNEEEVDLGPDPELARENFEKLRDL---Y 229

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +K R  FE++G +     +A   I       +   K  +++ + +R+ +++V   E+ I+
Sbjct: 230  NKARLIFEEKGRSHPDAKEAITEIGELFRTFKLMPKQFDRMVNNMRDMMDRVRVQERLIM 289

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            +       +P+  FIK F  NE N  W+D E      Y+  L    P I+    KL N++
Sbjct: 290  KQACQIAKLPKKTFIKHFANNESNGEWLDIEINAGEKYSDKLAECRPEIERSLNKLRNME 349

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
                L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 350  QTTGLSVERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 409

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 410  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 469

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 470  QMLQEMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTI 529

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
             +P D+A   S++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 530  ESPIDSATMESLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 589

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLEGK 1430
            QIEAKALRKLRHPSR   LK FL+ K
Sbjct: 590  QIEAKALRKLRHPSRSDLLKSFLDFK 615



 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 314/619 (50%), Positives = 412/619 (66%), Gaps = 46/619 (7%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V E   D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVCESAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TVD + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVDKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    EI++ +I+ G  D               ++EE+
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKYEAEEIRLSDIISGFFD---------------SDEEQ 172

Query: 222 ILIESS--SADLSTEQLE-------------------------KLKYESLIKFSNISFHF 254
             I ++   +DL+ EQL+                         +L  E+  K  ++   +
Sbjct: 173 FPIAATHIGSDLNDEQLKDEDVDLDDDDDDDSNEEEVDLGPDPELARENFEKLRDL---Y 229

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +K R  FE++G +     +A   I       +   K  +++ + +R+ +++V   E+ I+
Sbjct: 230 NKARLIFEEKGRSHPDAKEAITEIGELFRTFKLMPKQFDRMVNNMRDMMDRVRVQERLIM 289

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           +       +P+  FIK F  NE N  W+D E      Y+  L    P I+    KL N++
Sbjct: 290 KQACQIAKLPKKTFIKHFANNESNGEWLDIEINAGEKYSDKLAECRPEIERSLNKLRNME 349

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
               L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 350 QTTGLSVERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 409

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 410 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 469

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 470 QMLQEMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTI 529

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
            +P D+A   S++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 530 ESPIDSATMESLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 589

Query: 615 QIEAKALRKLR-PLAHDWL 632
           QIEAKALRKLR P   D L
Sbjct: 590 QIEAKALRKLRHPSRSDLL 608


>gi|417163224|ref|ZP_11998554.1| RNA polymerase sigma factor RpoD [Escherichia coli 99.0741]
 gi|386173715|gb|EIH45727.1| RNA polymerase sigma factor RpoD [Escherichia coli 99.0741]
          Length = 613

 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 414/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G ++
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSN 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 405/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G ++
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSN 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|87119778|ref|ZP_01075675.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
 gi|86165254|gb|EAQ66522.1| RNA polymerase sigma factor [Marinomonas sp. MED121]
          Length = 614

 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 312/625 (49%), Positives = 409/625 (65%), Gaps = 37/625 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K LI  GKE+GYLTF+E+ND LP+D+ D E +E II     M I V E+  D 
Sbjct: 3    DNQQSRLKELIAKGKEQGYLTFAEVNDHLPDDLSDPEQVEQIIAMINDMGIVVGEYAPDK 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            E L++    ++D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAK
Sbjct: 63   ENLLMEEGDSTDEAAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAIAK 122

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG ++++ A+S  P  +  +L A +K  + E ++ +I  G ID              
Sbjct: 123  RIEEGTREVMAAVSYYPGAVQTLLDAYEKSKEEEGRLSDIFSGFID-------------- 168

Query: 1006 NNNEEKILIESSSA--------DLSTEQLEKLKY--------------ESLIKFSNISFH 1043
             + EE +  ++           D STE+ E                  E+  +F  I  +
Sbjct: 169  GDGEEPVFEDAPLVEEVSEEELDKSTEESEDGDDDEDEEETDNGPDPEETARRFGEIERN 228

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
              ++    E          +    +S     I+   K  + L D +R+++++V + E+ I
Sbjct: 229  HTELLALLENHSRQDSIVKEKQEELSICFAPIKLVPKIFDDLVDRVRSRMDKVREQERII 288

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            +++ V K GMPR  F+K FP NE N+ W  ++      Y   L  N       Q+KL N+
Sbjct: 289  MQVCVRKAGMPRTEFLKRFPNNETNIQWFPDQIASGAGYAAALQENEAEFMRSQRKLRNI 348

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
              D  L + +L++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 349  SKDTGLTIVELKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 408

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 409  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 468

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G E  P  +A++M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+ 
Sbjct: 469  RQMLQEMGREATPEELAVRMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDG 528

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
              +P D A    +R     +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 529  AESPIDTATIEGLREATTSVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 588

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  RQIEAKALRKLRHPSRSEHLRSFLD 613



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 305/612 (49%), Positives = 400/612 (65%), Gaps = 37/612 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K LI  GKE+GYLTF+E+ND LP+D+ D E +E II     M I V E+  D 
Sbjct: 3   DNQQSRLKELIAKGKEQGYLTFAEVNDHLPDDLSDPEQVEQIIAMINDMGIVVGEYAPDK 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           E L++    ++D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAK
Sbjct: 63  ENLLMEEGDSTDEAAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAIAK 122

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG ++++ A+S  P  +  +L A +K  + E ++ +I  G ID              
Sbjct: 123 RIEEGTREVMAAVSYYPGAVQTLLDAYEKSKEEEGRLSDIFSGFID-------------- 168

Query: 216 NNNEEKILIESSSA--------DLSTEQLEKLKY--------------ESLIKFSNISFH 253
            + EE +  ++           D STE+ E                  E+  +F  I  +
Sbjct: 169 GDGEEPVFEDAPLVEEVSEEELDKSTEESEDGDDDEDEEETDNGPDPEETARRFGEIERN 228

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
             ++    E          +    +S     I+   K  + L D +R+++++V + E+ I
Sbjct: 229 HTELLALLENHSRQDSIVKEKQEELSICFAPIKLVPKIFDDLVDRVRSRMDKVREQERII 288

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           +++ V K GMPR  F+K FP NE N+ W  ++      Y   L  N       Q+KL N+
Sbjct: 289 MQVCVRKAGMPRTEFLKRFPNNETNIQWFPDQIASGAGYAAALQENEAEFMRSQRKLRNI 348

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
             D  L + +L++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 349 SKDTGLTIVELKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 408

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 409 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 468

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G E  P  +A++M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+ 
Sbjct: 469 RQMLQEMGREATPEELAVRMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDG 528

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
             +P D A    +R     +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 529 AESPIDTATIEGLREATTSVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 588

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 589 RQIEAKALRKLR 600


>gi|432378269|ref|ZP_19621254.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE12]
 gi|430896707|gb|ELC18935.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE12]
          Length = 613

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 411/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +      +    +           KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEENGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 402/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +      +    +           KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEENGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|77359315|ref|YP_338890.1| RNA polymerase sigma factor [Pseudoalteromonas haloplanktis TAC125]
 gi|76874226|emb|CAI85447.1| RNA polymerase sigma factor rpoD (Sigma-70) [Pseudoalteromonas
            haloplanktis TAC125]
          Length = 615

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 318/621 (51%), Positives = 413/621 (66%), Gaps = 35/621 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 1049
            I   +  ++LS +QL                           E+ + F N+   ++K R+
Sbjct: 175  ISATNIGSELSAKQLNDDDKDDDDSDEDDEDEEEVDTGPDPEEARVHFENLRDLYNKARE 234

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             FE +G +    + A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235  TFEAKGRSHPDSLAAIFEIGELFKTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQ 294

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
               +P+  F+K F  NE +  WVD E      Y+  L    P I     KL  +++   L
Sbjct: 295  IAKLPKKTFVKHFANNETDATWVDLEIAANEKYSAKLEEVKPEIIRSLNKLRVIESSTGL 354

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355  NIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP+P  +A +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475  MGREPNPEELAERMMMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535  SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHPSR   LK FL+ K
Sbjct: 595  ALRKLRHPSRSDLLKSFLDAK 615



 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 312/614 (50%), Positives = 406/614 (66%), Gaps = 36/614 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 222 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 259
           I   +  ++LS +QL                           E+ + F N+   ++K R+
Sbjct: 175 ISATNIGSELSAKQLNDDDKDDDDSDEDDEDEEEVDTGPDPEEARVHFENLRDLYNKARE 234

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
            FE +G +    + A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235 TFEAKGRSHPDSLAAIFEIGELFKTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQ 294

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
              +P+  F+K F  NE +  WVD E      Y+  L    P I     KL  +++   L
Sbjct: 295 IAKLPKKTFVKHFANNETDATWVDLEIAANEKYSAKLEEVKPEIIRSLNKLRVIESSTGL 354

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355 NIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP+P  +A +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475 MGREPNPEELAERMMMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535 SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 595 ALRKLRHPSRSDLL 608


>gi|406595570|ref|YP_006746700.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
 gi|407686426|ref|YP_006801599.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Balearic Sea
            AD45']
 gi|406372891|gb|AFS36146.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
 gi|407289806|gb|AFT94118.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Balearic Sea
            AD45']
          Length = 610

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 311/605 (51%), Positives = 414/605 (68%), Gaps = 11/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8    QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
                +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68   QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
              +  +++  P  I  +L   D     EI++ +I+ G +D N     +     +    + 
Sbjct: 128  NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDEQDLAPTATHVGSELSE 187

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEG---YNSESYIK 1063
             E     +    D S E    +  E +  +F+ +   + K R+  EK+G    +S + I 
Sbjct: 188  EELDDEDDDEDDDDSDEDDSGVDPELARERFTELREQYLKTREVIEKKGRAHADSRTQIN 247

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A +++  E    R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F 
Sbjct: 248  ALSDVFKE---FRLVPKQFDRMVKNMREMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFA 304

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  
Sbjct: 305  GNETSNAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSI 364

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 365  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 424

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M
Sbjct: 425  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERM 484

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++
Sbjct: 485  LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEV 544

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L
Sbjct: 545  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQL 604

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 605  RSFLD 609



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 304/592 (51%), Positives = 404/592 (68%), Gaps = 11/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8   QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
               +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68  QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
             +  +++  P  I  +L   D     EI++ +I+ G +D N     +     +    + 
Sbjct: 128 NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDEQDLAPTATHVGSELSE 187

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEG---YNSESYIK 273
            E     +    D S E    +  E +  +F+ +   + K R+  EK+G    +S + I 
Sbjct: 188 EELDDEDDDEDDDDSDEDDSGVDPELARERFTELREQYLKTREVIEKKGRAHADSRTQIN 247

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A +++  E    R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F 
Sbjct: 248 ALSDVFKE---FRLVPKQFDRMVKNMREMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFA 304

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  
Sbjct: 305 GNETSNAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSI 364

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 365 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 424

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M
Sbjct: 425 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERM 484

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++
Sbjct: 485 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEV 544

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 596


>gi|359443411|ref|ZP_09233253.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20429]
 gi|392533502|ref|ZP_10280639.1| RNA polymerase sigma factor [Pseudoalteromonas arctica A 37-1-2]
 gi|358034823|dbj|GAA69502.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20429]
          Length = 615

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 321/621 (51%), Positives = 414/621 (66%), Gaps = 35/621 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 1049
            I   +  ++LS +QL+  K                       E+ I F N+   ++K R 
Sbjct: 175  ISATNIGSELSAKQLDDDKDDKDDADSDDEDEEEVDTGPDPEEARIHFENLRDLYNKARD 234

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235  TFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQ 294

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
               +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L
Sbjct: 295  IAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTGL 354

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355  SIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475  MGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535  SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHPSR   LK FL+ K
Sbjct: 595  ALRKLRHPSRSDLLKSFLDAK 615



 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 315/614 (51%), Positives = 407/614 (66%), Gaps = 36/614 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 222 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 259
           I   +  ++LS +QL+  K                       E+ I F N+   ++K R 
Sbjct: 175 ISATNIGSELSAKQLDDDKDDKDDADSDDEDEEEVDTGPDPEEARIHFENLRDLYNKARD 234

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
            FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235 TFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAVQ 294

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
              +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L
Sbjct: 295 IAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTGL 354

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355 SIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475 MGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535 SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 595 ALRKLRHPSRSDLL 608


>gi|320539899|ref|ZP_08039558.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
            symbiotica str. Tucson]
 gi|320030085|gb|EFW12105.1| putative RNA polymerase, sigma 70 (sigma D) factor [Serratia
            symbiotica str. Tucson]
          Length = 607

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 307/618 (49%), Positives = 422/618 (68%), Gaps = 30/618 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+     +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D +           
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPD----------- 171

Query: 1005 KNNNEEKILIESS--SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
                EE I   ++   ++LSTE+ +    +     ++I     + + A  ++ Y +   +
Sbjct: 172  ---AEEDIAPTATHIGSELSTEEQDDEDDDDAEDDNSIDPELARQKFADLRDQYETTRLV 228

Query: 1063 -----KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
                 ++H + + E+L +       R   K  + L +++R  +++V   E+ I+++ V +
Sbjct: 229  IRKNSRSHASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRAMMDRVHTHERTIMKLCVEQ 288

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
            C MP+ +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L 
Sbjct: 289  CKMPKKNFVTLFAGNETSDVWFEKAQAMTKPWSEKLKDVAEDVQRSLQKLHQIEEETGLT 348

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 349  IEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 408

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 409  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 468

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED     P D+
Sbjct: 469  GREPMPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTFELPLDS 528

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 529  ATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 588

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FL+
Sbjct: 589  LRKLRHPSRSEVLRSFLD 606



 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 300/605 (49%), Positives = 413/605 (68%), Gaps = 30/605 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+     +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D +           
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPD----------- 171

Query: 215 KNNNEEKILIESS--SADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
               EE I   ++   ++LSTE+ +    +     ++I     + + A  ++ Y +   +
Sbjct: 172 ---AEEDIAPTATHIGSELSTEEQDDEDDDDAEDDNSIDPELARQKFADLRDQYETTRLV 228

Query: 273 -----KAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
                ++H + + E+L +       R   K  + L +++R  +++V   E+ I+++ V +
Sbjct: 229 IRKNSRSHASAAEEILKLSEVFKQFRLVPKQFDFLVNSMRAMMDRVHTHERTIMKLCVEQ 288

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
           C MP+ +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L 
Sbjct: 289 CKMPKKNFVTLFAGNETSDVWFEKAQAMTKPWSEKLKDVAEDVQRSLQKLHQIEEETGLT 348

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 349 IEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 408

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 409 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 468

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED     P D+
Sbjct: 469 GREPMPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTFELPLDS 528

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 529 ATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 588

Query: 621 LRKLR 625
           LRKLR
Sbjct: 589 LRKLR 593


>gi|167855425|ref|ZP_02478190.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219871370|ref|YP_002475745.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
 gi|167853419|gb|EDS24668.1| RNA polymerase sigma factor 70 [Haemophilus parasuis 29755]
 gi|219691574|gb|ACL32797.1| RNA polymerase sigma factor RpoD [Haemophilus parasuis SH0165]
          Length = 621

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 315/619 (50%), Positives = 418/619 (67%), Gaps = 19/619 (3%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            ++E  + + ++LI  G+E+GYLT SE++D LPE+++D + IE II+    M I V E   
Sbjct: 6    QLEEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDADQIEDIIQMINDMGIKVLETAP 65

Query: 885  DTETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            D + LML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 66   DADDLMLAGNIADEDVVEEATKV-LSTVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 124

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+ ++   I+  P  + E++   D++ +  +++ ++V   +D N   +  V   
Sbjct: 125  AKRIEEGINEVQCVIAEYPEALSELIARYDQVEEGTVRLSDLVTAFVDPNAVESTPVDDL 184

Query: 1004 -------NKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEK 1053
                   ++++    I  ES   + S +  +    +  +   KF+ +     K  +A +K
Sbjct: 185  DADLDEESESDTVADIDDESEDGESSGDGGDDNSIDPELAREKFTLLKEQHQKALQAIQK 244

Query: 1054 EGYNSE---SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
             G  S+     I+A ++I  E    R   K  + L +T++  + QV   E+QI    V  
Sbjct: 245  HGRTSKRSRDQIQALSDIFREF---RLVPKQFDLLVETMQKMMKQVRAEERQIQRYAVEY 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             GM +  FIKVF  NE++  W+D     +      L   + +I+     L  L+    L 
Sbjct: 302  AGMKKTDFIKVFQGNELSEAWIDKAINAKKGGVPKLANYVDNIRVNIANLQKLEETTGLT 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  +R+I  ++  GE+KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  ITQIREIGGRIADGELKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE 
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A KM MPE+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED ++  P D+
Sbjct: 482  GREATPEELAEKMGMPEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDSSLELPLDS 541

Query: 1351 ALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            A   S+R     +L   LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 542  ATAESLRIATNAVLEEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 601

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 602  ALRKLRHPSRSETLRSFLD 620



 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/606 (50%), Positives = 409/606 (67%), Gaps = 19/606 (3%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           ++E  + + ++LI  G+E+GYLT SE++D LPE+++D + IE II+    M I V E   
Sbjct: 6   QLEEQQSQLELLIAQGREQGYLTISEVHDHLPEELVDADQIEDIIQMINDMGIKVLETAP 65

Query: 95  DTETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           D + LML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 66  DADDLMLAGNIADEDVVEEATKV-LSTVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 124

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+ ++   I+  P  + E++   D++ +  +++ ++V   +D N   +  V   
Sbjct: 125 AKRIEEGINEVQCVIAEYPEALSELIARYDQVEEGTVRLSDLVTAFVDPNAVESTPVDDL 184

Query: 214 -------NKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSNISFHFDKMRKAFEK 263
                  ++++    I  ES   + S +  +    +  +   KF+ +     K  +A +K
Sbjct: 185 DADLDEESESDTVADIDDESEDGESSGDGGDDNSIDPELAREKFTLLKEQHQKALQAIQK 244

Query: 264 EGYNSE---SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
            G  S+     I+A ++I  E    R   K  + L +T++  + QV   E+QI    V  
Sbjct: 245 HGRTSKRSRDQIQALSDIFREF---RLVPKQFDLLVETMQKMMKQVRAEERQIQRYAVEY 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            GM +  FIKVF  NE++  W+D     +      L   + +I+     L  L+    L 
Sbjct: 302 AGMKKTDFIKVFQGNELSEAWIDKAINAKKGGVPKLANYVDNIRVNIANLQKLEETTGLT 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  +R+I  ++  GE+KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 ITQIREIGGRIADGELKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE 
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEM 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A KM MPE+KIRK++KIAKEP+SME+PVGDD+DSHLGDFIED ++  P D+
Sbjct: 482 GREATPEELAEKMGMPEDKIRKVLKIAKEPISMETPVGDDDDSHLGDFIEDSSLELPLDS 541

Query: 561 ALNASMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           A   S+R     +L   LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 542 ATAESLRIATNAVLEEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 601

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 602 ALRKLR 607


>gi|332163001|ref|YP_004299578.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica 105.5R(r)]
 gi|386309953|ref|YP_006006009.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica Y11]
 gi|418241497|ref|ZP_12868025.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica PhRBD_Ye1]
 gi|433550959|ref|ZP_20507002.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica IP 10393]
 gi|318604173|emb|CBY25671.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica Y11]
 gi|325667231|gb|ADZ43875.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica 105.5R(r)]
 gi|351779170|gb|EHB21291.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            palearctica PhRBD_Ye1]
 gi|431788058|emb|CCO70042.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica IP 10393]
          Length = 612

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 310/617 (50%), Positives = 417/617 (67%), Gaps = 23/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182  HVGSELSTEEMDDDDDEDEDDEEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239  ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295  KMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 595  RKLRHPSRSEVLRSFLD 611



 Score =  565 bits (1455), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/604 (50%), Positives = 408/604 (67%), Gaps = 23/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182 HVGSELSTEEMDDDDDEDEDDEEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239 ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295 KMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 622 RKLR 625
           RKLR
Sbjct: 595 RKLR 598


>gi|109897363|ref|YP_660618.1| RNA polymerase sigma-70 subunit RpoD [Pseudoalteromonas atlantica
            T6c]
 gi|109699644|gb|ABG39564.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoalteromonas atlantica
            T6c]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 309/621 (49%), Positives = 421/621 (67%), Gaps = 28/621 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 2    VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 61

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62   SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 122  RIEEGINQVQCSVAEYPEAITYLLDQWDMFEAEEIRLSDIIVGFVDPNEADNIAPTATHI 181

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 1057
             +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 182  GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 241

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                 K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 242  HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 301

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FIK F  NE + +W+            IL  + P ++EL+           K+  ++ + 
Sbjct: 302  FIKAFSGNETSTDWLFE----------ILASDAPYVEELKVHQEELERSIGKMNAVEDET 351

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 352  GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 411

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 412  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 471

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 472  QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 531

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 532  LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 591

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR  +L+ FL+
Sbjct: 592  AKALRKLRHPSRSEQLRSFLD 612



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 411/608 (67%), Gaps = 28/608 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 2   VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 61

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62  SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 122 RIEEGINQVQCSVAEYPEAITYLLDQWDMFEAEEIRLSDIIVGFVDPNEADNIAPTATHI 181

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 267
            +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 182 GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 241

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
                K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 242 HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 301

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FIK F  NE + +W+            IL  + P ++EL+           K+  ++ + 
Sbjct: 302 FIKAFSGNETSTDWLFE----------ILASDAPYVEELKVHQEELERSIGKMNAVEDET 351

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 352 GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 411

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 412 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 471

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 472 QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 531

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 532 LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 591

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 592 AKALRKLR 599


>gi|419138330|ref|ZP_13683121.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC5E]
 gi|377982750|gb|EHV46002.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC5E]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  +E    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLEDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  +E    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLEDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|187733221|ref|YP_001881829.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
 gi|187430213|gb|ACD09487.1| RNA polymerase sigma factor RpoD [Shigella boydii CDC 3083-94]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSTDDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSTDDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|15803609|ref|NP_289642.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EDL933]
 gi|15833204|ref|NP_311977.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            Sakai]
 gi|24114367|ref|NP_708877.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 301]
 gi|74313602|ref|YP_312021.1| RNA polymerase sigma factor RpoD [Shigella sonnei Ss046]
 gi|82545322|ref|YP_409269.1| RNA polymerase sigma factor RpoD [Shigella boydii Sb227]
 gi|110643311|ref|YP_671041.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110806954|ref|YP_690474.1| RNA polymerase sigma factor RpoD [Shigella flexneri 5 str. 8401]
 gi|157155497|ref|YP_001464528.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|168749343|ref|ZP_02774365.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4113]
 gi|168754040|ref|ZP_02779047.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4401]
 gi|168762022|ref|ZP_02787029.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4501]
 gi|168769477|ref|ZP_02794484.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4486]
 gi|168781203|ref|ZP_02806210.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4076]
 gi|168785943|ref|ZP_02810950.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC869]
 gi|168797660|ref|ZP_02822667.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC508]
 gi|170683578|ref|YP_001745339.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188493368|ref|ZP_03000638.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|191166845|ref|ZP_03028670.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|191172227|ref|ZP_03033770.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|193062048|ref|ZP_03043144.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|193067502|ref|ZP_03048470.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194427683|ref|ZP_03060230.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194431653|ref|ZP_03063944.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195937213|ref|ZP_03082595.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4024]
 gi|208809700|ref|ZP_03252037.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4206]
 gi|208813639|ref|ZP_03254968.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4045]
 gi|208820039|ref|ZP_03260359.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4042]
 gi|209399452|ref|YP_002272540.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4115]
 gi|209920540|ref|YP_002294624.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215488398|ref|YP_002330829.1| RNA polymerase sigma factor RpoD [Escherichia coli O127:H6 str.
            E2348/69]
 gi|217326836|ref|ZP_03442919.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            TW14588]
 gi|218555637|ref|YP_002388550.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI1]
 gi|218696772|ref|YP_002404439.1| RNA polymerase sigma factor RpoD [Escherichia coli 55989]
 gi|218701838|ref|YP_002409467.1| RNA polymerase sigma factor RpoD [Escherichia coli IAI39]
 gi|218706692|ref|YP_002414211.1| RNA polymerase sigma factor RpoD [Escherichia coli UMN026]
 gi|254795019|ref|YP_003079856.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            TW14359]
 gi|260845821|ref|YP_003223599.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str. 12009]
 gi|260857197|ref|YP_003231088.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            11368]
 gi|260869819|ref|YP_003236221.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str. 11128]
 gi|261228080|ref|ZP_05942361.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
            str. FRIK2000]
 gi|261254936|ref|ZP_05947469.1| RNA polymerase, sigma 70 factor [Escherichia coli O157:H7 str.
            FRIK966]
 gi|291284446|ref|YP_003501264.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            CB9615]
 gi|293406680|ref|ZP_06650606.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|293412444|ref|ZP_06655167.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|293416506|ref|ZP_06659145.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|293449405|ref|ZP_06663826.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|298382421|ref|ZP_06992018.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300818835|ref|ZP_07099041.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|300821663|ref|ZP_07101809.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300901451|ref|ZP_07119536.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300917392|ref|ZP_07134058.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300923730|ref|ZP_07139755.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300937447|ref|ZP_07152273.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300977468|ref|ZP_07173931.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|301021861|ref|ZP_07185824.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|307310308|ref|ZP_07589956.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|309793633|ref|ZP_07688059.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312968589|ref|ZP_07782798.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|331654667|ref|ZP_08355667.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331664680|ref|ZP_08365586.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331669908|ref|ZP_08370753.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331679143|ref|ZP_08379815.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331684720|ref|ZP_08385312.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332280114|ref|ZP_08392527.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|378711476|ref|YP_005276369.1| RNA polymerase sigma-70 subunit RpoD [Escherichia coli KO11FL]
 gi|383180244|ref|YP_005458249.1| RNA polymerase sigma factor RpoD [Shigella sonnei 53G]
 gi|384544669|ref|YP_005728733.1| putative DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Shigella flexneri 2002017]
 gi|386610458|ref|YP_006125944.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli W]
 gi|386625876|ref|YP_006145604.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O7:K1
            str. CE10]
 gi|386699972|ref|YP_006163809.1| RNA polymerase sigma factor RpoD [Escherichia coli KO11FL]
 gi|386710971|ref|YP_006174692.1| RNA polymerase sigma factor RpoD [Escherichia coli W]
 gi|387508474|ref|YP_006160730.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            RM12579]
 gi|387608796|ref|YP_006097652.1| RNA polymerase sigma-70 factor [Escherichia coli 042]
 gi|387884255|ref|YP_006314557.1| RNA polymerase sigma factor RpoD [Escherichia coli Xuzhou21]
 gi|407471039|ref|YP_006782518.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2009EL-2071]
 gi|407480304|ref|YP_006777453.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2011C-3493]
 gi|410480864|ref|YP_006768410.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2009EL-2050]
 gi|414577839|ref|ZP_11435013.1| RNA polymerase sigma factor rpoD [Shigella sonnei 3233-85]
 gi|415787258|ref|ZP_11493962.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa14]
 gi|415795491|ref|ZP_11497052.1| RNA polymerase sigma factor rpoD [Escherichia coli E128010]
 gi|415811312|ref|ZP_11503662.1| RNA polymerase sigma factor rpoD [Escherichia coli LT-68]
 gi|415820648|ref|ZP_11509755.1| RNA polymerase sigma factor rpoD [Escherichia coli OK1180]
 gi|415830552|ref|ZP_11516454.1| RNA polymerase sigma factor rpoD [Escherichia coli OK1357]
 gi|415839395|ref|ZP_11521137.1| RNA polymerase sigma factor rpoD [Escherichia coli RN587/1]
 gi|415845261|ref|ZP_11524859.1| RNA polymerase sigma factor rpoD [Shigella sonnei 53G]
 gi|415858131|ref|ZP_11532743.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2a str. 2457T]
 gi|415875021|ref|ZP_11541886.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 79-10]
 gi|416263801|ref|ZP_11640853.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae CDC 74-1112]
 gi|416285831|ref|ZP_11647980.1| RNA polymerase sigma factor RpoD [Shigella boydii ATCC 9905]
 gi|416305834|ref|ZP_11654371.1| RNA polymerase sigma factor RpoD [Shigella flexneri CDC 796-83]
 gi|416308376|ref|ZP_11655052.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str. 1044]
 gi|416322239|ref|ZP_11664087.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC1212]
 gi|416332480|ref|ZP_11670391.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str. 1125]
 gi|416340989|ref|ZP_11675710.1| RNA polymerase sigma factor RpoD [Escherichia coli EC4100B]
 gi|416777569|ref|ZP_11875220.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            G5101]
 gi|416788964|ref|ZP_11880146.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str.
            493-89]
 gi|416800874|ref|ZP_11885052.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str. H
            2687]
 gi|416811503|ref|ZP_11889860.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            3256-97]
 gi|416822011|ref|ZP_11894518.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str. USDA
            5905]
 gi|416832395|ref|ZP_11899614.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            LSU-61]
 gi|416899393|ref|ZP_11928875.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_7v]
 gi|417117219|ref|ZP_11968080.1| RNA polymerase sigma factor RpoD [Escherichia coli 1.2741]
 gi|417123394|ref|ZP_11972304.1| RNA polymerase sigma factor RpoD [Escherichia coli 97.0246]
 gi|417133760|ref|ZP_11978545.1| RNA polymerase sigma factor RpoD [Escherichia coli 5.0588]
 gi|417143436|ref|ZP_11985664.1| RNA polymerase sigma factor RpoD [Escherichia coli 97.0259]
 gi|417146915|ref|ZP_11987762.1| RNA polymerase sigma factor RpoD [Escherichia coli 1.2264]
 gi|417157382|ref|ZP_11995006.1| RNA polymerase sigma factor RpoD [Escherichia coli 96.0497]
 gi|417175298|ref|ZP_12005094.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.2608]
 gi|417186533|ref|ZP_12011676.1| RNA polymerase sigma factor RpoD [Escherichia coli 93.0624]
 gi|417201330|ref|ZP_12017901.1| RNA polymerase sigma factor RpoD [Escherichia coli 4.0522]
 gi|417210985|ref|ZP_12021402.1| RNA polymerase sigma factor RpoD [Escherichia coli JB1-95]
 gi|417222443|ref|ZP_12025883.1| RNA polymerase sigma factor RpoD [Escherichia coli 96.154]
 gi|417228199|ref|ZP_12029957.1| RNA polymerase sigma factor RpoD [Escherichia coli 5.0959]
 gi|417245201|ref|ZP_12038940.1| RNA polymerase sigma factor RpoD [Escherichia coli 9.0111]
 gi|417249230|ref|ZP_12041014.1| RNA polymerase sigma factor RpoD [Escherichia coli 4.0967]
 gi|417267812|ref|ZP_12055173.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.3884]
 gi|417281419|ref|ZP_12068719.1| RNA polymerase sigma factor RpoD [Escherichia coli 3003]
 gi|417296390|ref|ZP_12083637.1| RNA polymerase sigma factor RpoD [Escherichia coli 900105 (10e)]
 gi|417309598|ref|ZP_12096430.1| RNA polymerase sigma factor rpoD [Escherichia coli PCN033]
 gi|417582680|ref|ZP_12233481.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_B2F1]
 gi|417588180|ref|ZP_12238944.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_C165-02]
 gi|417593463|ref|ZP_12244155.1| RNA polymerase sigma factor rpoD [Escherichia coli 2534-86]
 gi|417598469|ref|ZP_12249098.1| RNA polymerase sigma factor rpoD [Escherichia coli 3030-1]
 gi|417603877|ref|ZP_12254443.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_94C]
 gi|417609745|ref|ZP_12260244.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_DG131-3]
 gi|417625114|ref|ZP_12275408.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_H.1.8]
 gi|417630522|ref|ZP_12280757.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_MHI813]
 gi|417668549|ref|ZP_12318090.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_O31]
 gi|417673975|ref|ZP_12323417.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|417673987|ref|ZP_12323428.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|417683635|ref|ZP_12332982.1| RNA polymerase sigma factor rpoD [Shigella boydii 3594-74]
 gi|417691382|ref|ZP_12340598.1| RNA polymerase sigma factor rpoD [Shigella boydii 5216-82]
 gi|417703536|ref|ZP_12352640.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-218]
 gi|417709119|ref|ZP_12358144.1| RNA polymerase sigma factor rpoD [Shigella flexneri VA-6]
 gi|417714160|ref|ZP_12363119.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-272]
 gi|417718845|ref|ZP_12367738.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-227]
 gi|417724698|ref|ZP_12373495.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-304]
 gi|417730015|ref|ZP_12378706.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-671]
 gi|417734971|ref|ZP_12383618.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2747-71]
 gi|417739940|ref|ZP_12388514.1| RNA polymerase sigma factor rpoD [Shigella flexneri 4343-70]
 gi|417744968|ref|ZP_12393490.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 2930-71]
 gi|417757430|ref|ZP_12405496.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2B]
 gi|417829545|ref|ZP_12476090.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri J1713]
 gi|417834450|ref|ZP_12480892.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            01-09591]
 gi|417865880|ref|ZP_12510923.1| hypothetical protein C22711_2811 [Escherichia coli O104:H4 str.
            C227-11]
 gi|418041038|ref|ZP_12679266.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W26]
 gi|418258499|ref|ZP_12881738.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 6603-63]
 gi|418268470|ref|ZP_12887190.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            sonnei str. Moseley]
 gi|418943946|ref|ZP_13497075.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H43 str. T22]
 gi|418998402|ref|ZP_13545988.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1A]
 gi|419003805|ref|ZP_13551318.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1B]
 gi|419009477|ref|ZP_13556896.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1C]
 gi|419015060|ref|ZP_13562401.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC1D]
 gi|419020109|ref|ZP_13567409.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1E]
 gi|419025460|ref|ZP_13572681.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC2A]
 gi|419030703|ref|ZP_13577852.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2C]
 gi|419036352|ref|ZP_13583429.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2D]
 gi|419041405|ref|ZP_13588424.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2E]
 gi|419047271|ref|ZP_13594205.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3A]
 gi|419052840|ref|ZP_13599707.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3B]
 gi|419058834|ref|ZP_13605636.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3C]
 gi|419064334|ref|ZP_13611056.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3D]
 gi|419071283|ref|ZP_13616896.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3E]
 gi|419077331|ref|ZP_13622834.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3F]
 gi|419082310|ref|ZP_13627756.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4A]
 gi|419088143|ref|ZP_13633495.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4B]
 gi|419093877|ref|ZP_13639159.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4C]
 gi|419099729|ref|ZP_13644922.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4D]
 gi|419105688|ref|ZP_13650813.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4E]
 gi|419111109|ref|ZP_13656162.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4F]
 gi|419116613|ref|ZP_13661625.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5A]
 gi|419122330|ref|ZP_13667273.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5B]
 gi|419127761|ref|ZP_13672636.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5C]
 gi|419133175|ref|ZP_13678004.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5D]
 gi|419176563|ref|ZP_13720375.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7B]
 gi|419198757|ref|ZP_13742053.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC8A]
 gi|419205270|ref|ZP_13748436.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8B]
 gi|419211511|ref|ZP_13754580.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8C]
 gi|419217383|ref|ZP_13760379.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8D]
 gi|419223206|ref|ZP_13766120.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8E]
 gi|419228634|ref|ZP_13771479.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9A]
 gi|419234137|ref|ZP_13776907.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9B]
 gi|419239603|ref|ZP_13782313.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9C]
 gi|419245091|ref|ZP_13787725.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9D]
 gi|419250967|ref|ZP_13793538.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9E]
 gi|419262961|ref|ZP_13805371.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10B]
 gi|419268694|ref|ZP_13811039.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10C]
 gi|419279699|ref|ZP_13821942.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10E]
 gi|419291224|ref|ZP_13833311.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC11A]
 gi|419296451|ref|ZP_13838492.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC11B]
 gi|419301979|ref|ZP_13843974.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11C]
 gi|419308018|ref|ZP_13849914.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11D]
 gi|419313082|ref|ZP_13854941.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11E]
 gi|419318479|ref|ZP_13860279.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC12A]
 gi|419324746|ref|ZP_13866435.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12B]
 gi|419330678|ref|ZP_13872276.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC12C]
 gi|419336187|ref|ZP_13877707.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12D]
 gi|419341585|ref|ZP_13883043.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12E]
 gi|419346810|ref|ZP_13888181.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13A]
 gi|419351276|ref|ZP_13892608.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13B]
 gi|419356696|ref|ZP_13897946.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13C]
 gi|419361729|ref|ZP_13902941.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13D]
 gi|419366755|ref|ZP_13907908.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13E]
 gi|419371636|ref|ZP_13912746.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC14A]
 gi|419377129|ref|ZP_13918150.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14B]
 gi|419382465|ref|ZP_13923409.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14C]
 gi|419387755|ref|ZP_13928626.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14D]
 gi|419393214|ref|ZP_13934017.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15A]
 gi|419398320|ref|ZP_13939083.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15B]
 gi|419403602|ref|ZP_13944322.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15C]
 gi|419408758|ref|ZP_13949444.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15D]
 gi|419414305|ref|ZP_13954944.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15E]
 gi|419805810|ref|ZP_14330936.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli AI27]
 gi|419864343|ref|ZP_14386804.1| RNA polymerase sigma factor RpoD [Escherichia coli O103:H25 str.
            CVM9340]
 gi|419871026|ref|ZP_14393090.1| RNA polymerase sigma factor RpoD [Escherichia coli O103:H2 str.
            CVM9450]
 gi|419878008|ref|ZP_14399489.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9534]
 gi|419885376|ref|ZP_14406142.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9545]
 gi|419891727|ref|ZP_14411770.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9570]
 gi|419896277|ref|ZP_14415995.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9574]
 gi|419898963|ref|ZP_14418497.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM9942]
 gi|419910840|ref|ZP_14429348.1| hypothetical protein ECO10026_27460 [Escherichia coli O26:H11 str.
            CVM10026]
 gi|419919741|ref|ZP_14437882.1| RNA polymerase sigma factor RpoD [Escherichia coli KD2]
 gi|419923925|ref|ZP_14441824.1| RNA polymerase sigma factor RpoD [Escherichia coli 541-15]
 gi|419927501|ref|ZP_14445237.1| RNA polymerase sigma factor RpoD [Escherichia coli 541-1]
 gi|419934997|ref|ZP_14452085.1| RNA polymerase sigma factor RpoD [Escherichia coli 576-1]
 gi|419948070|ref|ZP_14464376.1| RNA polymerase sigma factor RpoD [Escherichia coli CUMT8]
 gi|420091977|ref|ZP_14603702.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9602]
 gi|420096328|ref|ZP_14607730.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9634]
 gi|420102817|ref|ZP_14613764.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9455]
 gi|420110987|ref|ZP_14620865.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9553]
 gi|420116177|ref|ZP_14625631.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10021]
 gi|420118494|ref|ZP_14627815.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10030]
 gi|420128496|ref|ZP_14637051.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10224]
 gi|420134324|ref|ZP_14642434.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM9952]
 gi|420271305|ref|ZP_14773658.1| RNA polymerase sigma factor [Escherichia coli PA22]
 gi|420277110|ref|ZP_14779391.1| RNA polymerase sigma factor [Escherichia coli PA40]
 gi|420282031|ref|ZP_14784264.1| RNA polymerase sigma factor [Escherichia coli TW06591]
 gi|420288470|ref|ZP_14790654.1| RNA polymerase sigma factor [Escherichia coli TW10246]
 gi|420294180|ref|ZP_14796294.1| RNA polymerase sigma factor [Escherichia coli TW11039]
 gi|420300034|ref|ZP_14802079.1| RNA polymerase sigma factor [Escherichia coli TW09109]
 gi|420306068|ref|ZP_14808057.1| RNA polymerase sigma factor [Escherichia coli TW10119]
 gi|420311470|ref|ZP_14813399.1| RNA polymerase sigma factor [Escherichia coli EC1738]
 gi|420317120|ref|ZP_14818993.1| RNA polymerase sigma factor [Escherichia coli EC1734]
 gi|420322028|ref|ZP_14823852.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2850-71]
 gi|420326914|ref|ZP_14828661.1| RNA polymerase sigma factor rpoD [Shigella flexneri CCH060]
 gi|420332987|ref|ZP_14834633.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-1770]
 gi|420337730|ref|ZP_14839292.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-315]
 gi|420343456|ref|ZP_14844921.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-404]
 gi|420353803|ref|ZP_14854907.1| RNA polymerase sigma factor rpoD [Shigella boydii 4444-74]
 gi|420360400|ref|ZP_14861358.1| RNA polymerase sigma factor rpoD [Shigella sonnei 3226-85]
 gi|420365116|ref|ZP_14865985.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            sonnei 4822-66]
 gi|420381988|ref|ZP_14881428.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 225-75]
 gi|420393174|ref|ZP_14892420.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli EPEC C342-62]
 gi|421684191|ref|ZP_16123980.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 1485-80]
 gi|421814100|ref|ZP_16249808.1| RNA polymerase sigma factor [Escherichia coli 8.0416]
 gi|421819896|ref|ZP_16255384.1| RNA polymerase sigma factor rpoD [Escherichia coli 10.0821]
 gi|421825907|ref|ZP_16261261.1| RNA polymerase sigma factor [Escherichia coli FRIK920]
 gi|421832623|ref|ZP_16267905.1| RNA polymerase sigma factor [Escherichia coli PA7]
 gi|422332548|ref|ZP_16413561.1| RNA polymerase sigma factor rpoD [Escherichia coli 4_1_47FAA]
 gi|422353816|ref|ZP_16434565.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 117-3]
 gi|422376691|ref|ZP_16456940.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 60-1]
 gi|422760537|ref|ZP_16814297.1| RNA polymerase sigma proteinRpoD [Escherichia coli E1167]
 gi|422775684|ref|ZP_16829339.1| RNA polymerase sigma protein RpoD [Escherichia coli H120]
 gi|422779962|ref|ZP_16832747.1| RNA polymerase sigma proteinRpoD [Escherichia coli TW10509]
 gi|422801019|ref|ZP_16849516.1| RNA polymerase sigma proteinRpoD [Escherichia coli M863]
 gi|422827522|ref|ZP_16875696.1| RNA polymerase sigma factor rpoD [Escherichia coli B093]
 gi|422833577|ref|ZP_16881643.1| RNA polymerase sigma factor rpoD [Escherichia coli E101]
 gi|422959836|ref|ZP_16971471.1| RNA polymerase sigma factor rpoD [Escherichia coli H494]
 gi|422969765|ref|ZP_16973558.1| RNA polymerase sigma factor rpoD [Escherichia coli TA124]
 gi|422989271|ref|ZP_16980043.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            C227-11]
 gi|422996166|ref|ZP_16986929.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            C236-11]
 gi|423001316|ref|ZP_16992069.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            09-7901]
 gi|423004975|ref|ZP_16995720.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            04-8351]
 gi|423011480|ref|ZP_17002213.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-3677]
 gi|423020710|ref|ZP_17011417.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4404]
 gi|423025872|ref|ZP_17016567.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4522]
 gi|423031692|ref|ZP_17022378.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4623]
 gi|423034564|ref|ZP_17025242.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C1]
 gi|423039692|ref|ZP_17030361.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C2]
 gi|423046375|ref|ZP_17037034.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C3]
 gi|423054912|ref|ZP_17043718.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C4]
 gi|423056904|ref|ZP_17045703.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C5]
 gi|423707368|ref|ZP_17681748.1| RNA polymerase sigma factor rpoD [Escherichia coli B799]
 gi|423727017|ref|ZP_17700935.1| RNA polymerase sigma factor [Escherichia coli PA31]
 gi|424079224|ref|ZP_17816194.1| RNA polymerase sigma factor [Escherichia coli FDA505]
 gi|424085682|ref|ZP_17822171.1| RNA polymerase sigma factor [Escherichia coli FDA517]
 gi|424092084|ref|ZP_17828015.1| RNA polymerase sigma factor [Escherichia coli FRIK1996]
 gi|424098750|ref|ZP_17834028.1| RNA polymerase sigma factor [Escherichia coli FRIK1985]
 gi|424104965|ref|ZP_17839710.1| RNA polymerase sigma factor [Escherichia coli FRIK1990]
 gi|424111614|ref|ZP_17845846.1| RNA polymerase sigma factor [Escherichia coli 93-001]
 gi|424117550|ref|ZP_17851385.1| RNA polymerase sigma factor [Escherichia coli PA3]
 gi|424123740|ref|ZP_17857049.1| RNA polymerase sigma factor [Escherichia coli PA5]
 gi|424129891|ref|ZP_17862795.1| RNA polymerase sigma factor [Escherichia coli PA9]
 gi|424136216|ref|ZP_17868665.1| RNA polymerase sigma factor [Escherichia coli PA10]
 gi|424142763|ref|ZP_17874632.1| RNA polymerase sigma factor [Escherichia coli PA14]
 gi|424149166|ref|ZP_17880538.1| RNA polymerase sigma factor [Escherichia coli PA15]
 gi|424155001|ref|ZP_17885934.1| RNA polymerase sigma factor [Escherichia coli PA24]
 gi|424253617|ref|ZP_17891497.1| RNA polymerase sigma factor [Escherichia coli PA25]
 gi|424332095|ref|ZP_17897403.1| RNA polymerase sigma factor [Escherichia coli PA28]
 gi|424451450|ref|ZP_17903122.1| RNA polymerase sigma factor [Escherichia coli PA32]
 gi|424457641|ref|ZP_17908753.1| RNA polymerase sigma factor [Escherichia coli PA33]
 gi|424464096|ref|ZP_17914477.1| RNA polymerase sigma factor [Escherichia coli PA39]
 gi|424470402|ref|ZP_17920216.1| RNA polymerase sigma factor [Escherichia coli PA41]
 gi|424476913|ref|ZP_17926227.1| RNA polymerase sigma factor [Escherichia coli PA42]
 gi|424482670|ref|ZP_17931646.1| RNA polymerase sigma factor [Escherichia coli TW07945]
 gi|424488852|ref|ZP_17937399.1| RNA polymerase sigma factor [Escherichia coli TW09098]
 gi|424495477|ref|ZP_17943113.1| RNA polymerase sigma factor [Escherichia coli TW09195]
 gi|424502202|ref|ZP_17949090.1| RNA polymerase sigma factor [Escherichia coli EC4203]
 gi|424508454|ref|ZP_17954840.1| RNA polymerase sigma factor [Escherichia coli EC4196]
 gi|424515805|ref|ZP_17960443.1| RNA polymerase sigma factor [Escherichia coli TW14313]
 gi|424522008|ref|ZP_17966122.1| RNA polymerase sigma factor [Escherichia coli TW14301]
 gi|424527886|ref|ZP_17971599.1| RNA polymerase sigma factor [Escherichia coli EC4421]
 gi|424534031|ref|ZP_17977376.1| RNA polymerase sigma factor [Escherichia coli EC4422]
 gi|424540086|ref|ZP_17983026.1| RNA polymerase sigma factor [Escherichia coli EC4013]
 gi|424546211|ref|ZP_17988582.1| RNA polymerase sigma factor [Escherichia coli EC4402]
 gi|424552435|ref|ZP_17994277.1| RNA polymerase sigma factor [Escherichia coli EC4439]
 gi|424558609|ref|ZP_18000017.1| RNA polymerase sigma factor [Escherichia coli EC4436]
 gi|424564948|ref|ZP_18005948.1| RNA polymerase sigma factor [Escherichia coli EC4437]
 gi|424571090|ref|ZP_18011636.1| RNA polymerase sigma factor [Escherichia coli EC4448]
 gi|424577247|ref|ZP_18017298.1| RNA polymerase sigma factor [Escherichia coli EC1845]
 gi|424583069|ref|ZP_18022712.1| RNA polymerase sigma factor [Escherichia coli EC1863]
 gi|424746385|ref|ZP_18174624.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CFSAN001629]
 gi|424757735|ref|ZP_18185468.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CFSAN001630]
 gi|424769731|ref|ZP_18196955.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CFSAN001632]
 gi|424839339|ref|ZP_18263976.1| RNA polymerase sigma factor RpoD [Shigella flexneri 5a str. M90T]
 gi|425099737|ref|ZP_18502467.1| RNA polymerase sigma factor rpoD [Escherichia coli 3.4870]
 gi|425105837|ref|ZP_18508152.1| RNA polymerase sigma factor rpoD [Escherichia coli 5.2239]
 gi|425111850|ref|ZP_18513768.1| RNA polymerase sigma factor [Escherichia coli 6.0172]
 gi|425127772|ref|ZP_18528937.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.0586]
 gi|425133512|ref|ZP_18534358.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.2524]
 gi|425140093|ref|ZP_18540471.1| RNA polymerase sigma factor [Escherichia coli 10.0833]
 gi|425145803|ref|ZP_18545796.1| RNA polymerase sigma factor rpoD [Escherichia coli 10.0869]
 gi|425151920|ref|ZP_18551531.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.0221]
 gi|425157792|ref|ZP_18557052.1| RNA polymerase sigma factor [Escherichia coli PA34]
 gi|425164143|ref|ZP_18563027.1| RNA polymerase sigma factor [Escherichia coli FDA506]
 gi|425169886|ref|ZP_18568357.1| RNA polymerase sigma factor [Escherichia coli FDA507]
 gi|425175946|ref|ZP_18574063.1| RNA polymerase sigma factor [Escherichia coli FDA504]
 gi|425181987|ref|ZP_18579679.1| RNA polymerase sigma factor [Escherichia coli FRIK1999]
 gi|425188253|ref|ZP_18585523.1| RNA polymerase sigma factor [Escherichia coli FRIK1997]
 gi|425195019|ref|ZP_18591785.1| RNA polymerase sigma factor [Escherichia coli NE1487]
 gi|425201495|ref|ZP_18597700.1| RNA polymerase sigma factor [Escherichia coli NE037]
 gi|425207880|ref|ZP_18603674.1| RNA polymerase sigma factor [Escherichia coli FRIK2001]
 gi|425213635|ref|ZP_18609033.1| RNA polymerase sigma factor [Escherichia coli PA4]
 gi|425219757|ref|ZP_18614717.1| RNA polymerase sigma factor [Escherichia coli PA23]
 gi|425226306|ref|ZP_18620770.1| RNA polymerase sigma factor [Escherichia coli PA49]
 gi|425232566|ref|ZP_18626603.1| RNA polymerase sigma factor [Escherichia coli PA45]
 gi|425238489|ref|ZP_18632206.1| RNA polymerase sigma factor [Escherichia coli TT12B]
 gi|425244726|ref|ZP_18638029.1| RNA polymerase sigma factor [Escherichia coli MA6]
 gi|425250919|ref|ZP_18643858.1| RNA polymerase sigma factor [Escherichia coli 5905]
 gi|425256701|ref|ZP_18649211.1| RNA polymerase sigma factor [Escherichia coli CB7326]
 gi|425262953|ref|ZP_18654954.1| RNA polymerase sigma factor [Escherichia coli EC96038]
 gi|425268951|ref|ZP_18660579.1| RNA polymerase sigma factor [Escherichia coli 5412]
 gi|425279473|ref|ZP_18670702.1| RNA polymerase sigma factor [Escherichia coli ARS4.2123]
 gi|425296404|ref|ZP_18686571.1| RNA polymerase sigma factor [Escherichia coli PA38]
 gi|425313094|ref|ZP_18702270.1| RNA polymerase sigma factor [Escherichia coli EC1735]
 gi|425319078|ref|ZP_18707863.1| RNA polymerase sigma factor [Escherichia coli EC1736]
 gi|425325169|ref|ZP_18713523.1| RNA polymerase sigma factor [Escherichia coli EC1737]
 gi|425331536|ref|ZP_18719371.1| RNA polymerase sigma factor [Escherichia coli EC1846]
 gi|425337714|ref|ZP_18725068.1| RNA polymerase sigma factor [Escherichia coli EC1847]
 gi|425344025|ref|ZP_18730912.1| RNA polymerase sigma factor [Escherichia coli EC1848]
 gi|425349833|ref|ZP_18736298.1| RNA polymerase sigma factor [Escherichia coli EC1849]
 gi|425356134|ref|ZP_18742199.1| RNA polymerase sigma factor [Escherichia coli EC1850]
 gi|425362098|ref|ZP_18747742.1| RNA polymerase sigma factor [Escherichia coli EC1856]
 gi|425368313|ref|ZP_18753435.1| RNA polymerase sigma factor [Escherichia coli EC1862]
 gi|425374631|ref|ZP_18759269.1| RNA polymerase sigma factor [Escherichia coli EC1864]
 gi|425381334|ref|ZP_18765334.1| RNA polymerase sigma factor [Escherichia coli EC1865]
 gi|425387522|ref|ZP_18771077.1| RNA polymerase sigma factor [Escherichia coli EC1866]
 gi|425394173|ref|ZP_18777278.1| RNA polymerase sigma factor [Escherichia coli EC1868]
 gi|425400314|ref|ZP_18783015.1| RNA polymerase sigma factor [Escherichia coli EC1869]
 gi|425406401|ref|ZP_18788619.1| RNA polymerase sigma factor [Escherichia coli EC1870]
 gi|425412784|ref|ZP_18794544.1| RNA polymerase sigma factor [Escherichia coli NE098]
 gi|425419101|ref|ZP_18800368.1| RNA polymerase sigma factor [Escherichia coli FRIK523]
 gi|425423937|ref|ZP_18805096.1| RNA polymerase sigma factor [Escherichia coli 0.1288]
 gi|425430372|ref|ZP_18810979.1| RNA polymerase sigma factor [Escherichia coli 0.1304]
 gi|428948803|ref|ZP_19021077.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.1467]
 gi|428954879|ref|ZP_19026673.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.1042]
 gi|428960870|ref|ZP_19032162.1| RNA polymerase sigma factor rpoD [Escherichia coli 89.0511]
 gi|428967484|ref|ZP_19038194.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.0091]
 gi|428973222|ref|ZP_19043545.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.0039]
 gi|428979649|ref|ZP_19049468.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.2281]
 gi|428985407|ref|ZP_19054798.1| RNA polymerase sigma factor rpoD [Escherichia coli 93.0055]
 gi|428991598|ref|ZP_19060584.1| RNA polymerase sigma factor rpoD [Escherichia coli 93.0056]
 gi|428997483|ref|ZP_19066076.1| RNA polymerase sigma factor rpoD [Escherichia coli 94.0618]
 gi|429003754|ref|ZP_19071854.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0183]
 gi|429009853|ref|ZP_19077310.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.1288]
 gi|429016377|ref|ZP_19083257.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0943]
 gi|429022119|ref|ZP_19088638.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0428]
 gi|429028273|ref|ZP_19094265.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0427]
 gi|429034451|ref|ZP_19099971.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0939]
 gi|429040535|ref|ZP_19105633.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0932]
 gi|429046330|ref|ZP_19111040.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0107]
 gi|429051807|ref|ZP_19116370.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0003]
 gi|429057234|ref|ZP_19121532.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.1742]
 gi|429062736|ref|ZP_19126729.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0007]
 gi|429068991|ref|ZP_19132446.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0672]
 gi|429074934|ref|ZP_19138182.1| RNA polymerase sigma factor [Escherichia coli 99.0678]
 gi|429080133|ref|ZP_19143266.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0713]
 gi|429720734|ref|ZP_19255657.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9450]
 gi|429772634|ref|ZP_19304652.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02030]
 gi|429777585|ref|ZP_19309555.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02033-1]
 gi|429786306|ref|ZP_19318199.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02092]
 gi|429787250|ref|ZP_19319140.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02093]
 gi|429793046|ref|ZP_19324892.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02281]
 gi|429799625|ref|ZP_19331419.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02318]
 gi|429803241|ref|ZP_19334999.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02913]
 gi|429807881|ref|ZP_19339602.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-03439]
 gi|429813581|ref|ZP_19345258.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-04080]
 gi|429818792|ref|ZP_19350424.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-03943]
 gi|429828167|ref|ZP_19359190.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0109]
 gi|429834551|ref|ZP_19364855.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0010]
 gi|429905140|ref|ZP_19371117.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9990]
 gi|429909276|ref|ZP_19375239.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9941]
 gi|429915147|ref|ZP_19381093.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4984]
 gi|429920194|ref|ZP_19386122.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-5604]
 gi|429925998|ref|ZP_19391910.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4986]
 gi|429929934|ref|ZP_19395835.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4987]
 gi|429936472|ref|ZP_19402357.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4988]
 gi|429942152|ref|ZP_19408025.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-5603]
 gi|429944836|ref|ZP_19410697.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-6006]
 gi|429952392|ref|ZP_19418237.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec12-0465]
 gi|429955747|ref|ZP_19421577.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec12-0466]
 gi|432393669|ref|ZP_19636493.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE21]
 gi|432403455|ref|ZP_19646200.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE26]
 gi|432427714|ref|ZP_19670199.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE181]
 gi|432451317|ref|ZP_19693575.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE193]
 gi|432462419|ref|ZP_19704553.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE204]
 gi|432472428|ref|ZP_19714466.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE206]
 gi|432477412|ref|ZP_19719402.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE208]
 gi|432482404|ref|ZP_19724355.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE210]
 gi|432490860|ref|ZP_19732724.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE213]
 gi|432519274|ref|ZP_19756454.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE228]
 gi|432527902|ref|ZP_19764983.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE233]
 gi|432535419|ref|ZP_19772384.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE234]
 gi|432544822|ref|ZP_19781657.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE236]
 gi|432550304|ref|ZP_19787064.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE237]
 gi|432603916|ref|ZP_19840147.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE66]
 gi|432618328|ref|ZP_19854433.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE75]
 gi|432632952|ref|ZP_19868873.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE80]
 gi|432642641|ref|ZP_19878468.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE83]
 gi|432676188|ref|ZP_19911640.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE142]
 gi|432681796|ref|ZP_19917156.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE143]
 gi|432714928|ref|ZP_19949956.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE8]
 gi|432720214|ref|ZP_19955179.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE9]
 gi|432751545|ref|ZP_19986128.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE29]
 gi|432766435|ref|ZP_20000852.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE48]
 gi|432767447|ref|ZP_20001841.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE50]
 gi|432776158|ref|ZP_20010421.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE54]
 gi|432794299|ref|ZP_20028381.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE78]
 gi|432795816|ref|ZP_20029857.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE79]
 gi|432807333|ref|ZP_20041248.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE91]
 gi|432810781|ref|ZP_20044659.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE101]
 gi|432816852|ref|ZP_20050613.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE115]
 gi|432828707|ref|ZP_20062325.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE135]
 gi|432836029|ref|ZP_20069563.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE136]
 gi|432840886|ref|ZP_20074346.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE140]
 gi|432854223|ref|ZP_20082768.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE144]
 gi|432864989|ref|ZP_20088237.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE146]
 gi|432870539|ref|ZP_20090996.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE147]
 gi|432888381|ref|ZP_20102133.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE158]
 gi|432914569|ref|ZP_20119985.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE190]
 gi|432936259|ref|ZP_20135393.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE184]
 gi|432949141|ref|ZP_20144064.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE196]
 gi|432963533|ref|ZP_20152952.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE202]
 gi|432969138|ref|ZP_20158050.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE203]
 gi|433020207|ref|ZP_20208373.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE105]
 gi|433034964|ref|ZP_20222664.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE112]
 gi|433044619|ref|ZP_20232106.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE117]
 gi|433049508|ref|ZP_20236846.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE120]
 gi|433064529|ref|ZP_20251440.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE125]
 gi|433069395|ref|ZP_20256170.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE128]
 gi|433079267|ref|ZP_20265787.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE131]
 gi|433093456|ref|ZP_20279714.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE138]
 gi|433160187|ref|ZP_20345014.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE177]
 gi|433179904|ref|ZP_20364291.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE82]
 gi|433195117|ref|ZP_20379096.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE90]
 gi|433204785|ref|ZP_20388541.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE95]
 gi|442593611|ref|ZP_21011549.1| RNA polymerase sigma factor RpoD [Escherichia coli O10:K5(L):H4 str.
            ATCC 23506]
 gi|444926689|ref|ZP_21245965.1| RNA polymerase sigma factor rpoD [Escherichia coli 09BKT078844]
 gi|444932376|ref|ZP_21251398.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0814]
 gi|444937801|ref|ZP_21256560.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0815]
 gi|444943394|ref|ZP_21261897.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0816]
 gi|444948854|ref|ZP_21267159.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0839]
 gi|444954501|ref|ZP_21272580.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0848]
 gi|444959972|ref|ZP_21277809.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1753]
 gi|444965162|ref|ZP_21282745.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1775]
 gi|444971150|ref|ZP_21288503.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1793]
 gi|444976402|ref|ZP_21293507.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1805]
 gi|444981842|ref|ZP_21298746.1| RNA polymerase sigma factor rpoD [Escherichia coli ATCC 700728]
 gi|444987201|ref|ZP_21303976.1| RNA polymerase sigma factor rpoD [Escherichia coli PA11]
 gi|444992512|ref|ZP_21309152.1| RNA polymerase sigma factor rpoD [Escherichia coli PA19]
 gi|444997797|ref|ZP_21314292.1| RNA polymerase sigma factor rpoD [Escherichia coli PA13]
 gi|445003393|ref|ZP_21319778.1| RNA polymerase sigma factor rpoD [Escherichia coli PA2]
 gi|445008764|ref|ZP_21325001.1| RNA polymerase sigma factor rpoD [Escherichia coli PA47]
 gi|445013927|ref|ZP_21330030.1| RNA polymerase sigma factor rpoD [Escherichia coli PA48]
 gi|445019807|ref|ZP_21335769.1| RNA polymerase sigma factor rpoD [Escherichia coli PA8]
 gi|445025211|ref|ZP_21341031.1| RNA polymerase sigma factor rpoD [Escherichia coli 7.1982]
 gi|445030632|ref|ZP_21346301.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1781]
 gi|445036066|ref|ZP_21351591.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1762]
 gi|445041690|ref|ZP_21357058.1| RNA polymerase sigma factor rpoD [Escherichia coli PA35]
 gi|445046951|ref|ZP_21362197.1| RNA polymerase sigma factor rpoD [Escherichia coli 3.4880]
 gi|445052467|ref|ZP_21367494.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0083]
 gi|445058163|ref|ZP_21373020.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0670]
 gi|450204427|ref|ZP_21893609.1| RNA polymerase sigma factor RpoD [Escherichia coli SEPT362]
 gi|450222264|ref|ZP_21896787.1| RNA polymerase sigma factor RpoD [Escherichia coli O08]
 gi|452968080|ref|ZP_21966307.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4009]
 gi|12517649|gb|AAG58201.1|AE005536_2 RNA polymerase, sigma(70) factor; regulation of proteins induced at
            high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|13363423|dbj|BAB37373.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli O157:H7 str.
            Sakai]
 gi|24053533|gb|AAN44584.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|73857079|gb|AAZ89786.1| RNA polymerase, sigma(70) factor [Shigella sonnei Ss046]
 gi|81246733|gb|ABB67441.1| RNA polymerase sigma(70) factor [Shigella boydii Sb227]
 gi|110344903|gb|ABG71140.1| RNA polymerase sigma factor RpoD [Escherichia coli 536]
 gi|110616502|gb|ABF05169.1| RpoD protein [Shigella flexneri 5 str. 8401]
 gi|157077527|gb|ABV17235.1| RNA polymerase sigma factor RpoD [Escherichia coli E24377A]
 gi|170521296|gb|ACB19474.1| RNA polymerase sigma factor RpoD [Escherichia coli SMS-3-5]
 gi|188016365|gb|EDU54487.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4113]
 gi|188488567|gb|EDU63670.1| RNA polymerase sigma factor RpoD [Escherichia coli 53638]
 gi|189000977|gb|EDU69963.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4076]
 gi|189358698|gb|EDU77117.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4401]
 gi|189361403|gb|EDU79822.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4486]
 gi|189367616|gb|EDU86032.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4501]
 gi|189374126|gb|EDU92542.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC869]
 gi|189379773|gb|EDU98189.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC508]
 gi|190903087|gb|EDV62811.1| RNA polymerase sigma factor RpoD [Escherichia coli B7A]
 gi|190907537|gb|EDV67133.1| RNA polymerase sigma factor RpoD [Escherichia coli F11]
 gi|192932268|gb|EDV84866.1| RNA polymerase sigma factor RpoD [Escherichia coli E22]
 gi|192959459|gb|EDV89894.1| RNA polymerase sigma factor RpoD [Escherichia coli E110019]
 gi|194414191|gb|EDX30466.1| RNA polymerase sigma factor RpoD [Escherichia coli B171]
 gi|194420009|gb|EDX36087.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae 1012]
 gi|195183229|dbj|BAG66772.1| RNA polymerase, sigma(70) factor [Escherichia coli O111:H-]
 gi|208729501|gb|EDZ79102.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4206]
 gi|208734916|gb|EDZ83603.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4045]
 gi|208740162|gb|EDZ87844.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4042]
 gi|209160852|gb|ACI38285.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC4115]
 gi|209759228|gb|ACI77926.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759230|gb|ACI77927.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759232|gb|ACI77928.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759234|gb|ACI77929.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209759236|gb|ACI77930.1| RNA polymerase sigma 70 factor RpoD [Escherichia coli]
 gi|209913799|dbj|BAG78873.1| RNA polymerase sigma factor RpoD [Escherichia coli SE11]
 gi|215266470|emb|CAS10908.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O127:H6
            str. E2348/69]
 gi|217319203|gb|EEC27628.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            TW14588]
 gi|218353504|emb|CAU99623.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli 55989]
 gi|218362405|emb|CAR00029.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI1]
 gi|218371824|emb|CAR19679.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli IAI39]
 gi|218433789|emb|CAR14706.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli UMN026]
 gi|254594419|gb|ACT73780.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O157:H7
            str. TW14359]
 gi|257755846|dbj|BAI27348.1| RNA polymerase, sigma 70 factor [Escherichia coli O26:H11 str. 11368]
 gi|257760968|dbj|BAI32465.1| RNA polymerase, sigma 70 factor [Escherichia coli O103:H2 str. 12009]
 gi|257766175|dbj|BAI37670.1| RNA polymerase, sigma 70 factor [Escherichia coli O111:H- str. 11128]
 gi|281602456|gb|ADA75440.1| putative DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Shigella flexneri 2002017]
 gi|284923096|emb|CBG36189.1| RNA polymerase sigma-70 factor [Escherichia coli 042]
 gi|290764319|gb|ADD58280.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            CB9615]
 gi|291322495|gb|EFE61924.1| RNA polymerase primary sigma factor [Escherichia coli B088]
 gi|291426686|gb|EFE99718.1| RNA polymerase sigma factor RpoD [Escherichia coli FVEC1412]
 gi|291431862|gb|EFF04845.1| RNA polymerase primary sigma factor [Escherichia coli B185]
 gi|291469215|gb|EFF11706.1| RNA polymerase sigma factor rpoD [Escherichia coli B354]
 gi|298277561|gb|EFI19077.1| RNA polymerase sigma factor rpoD [Escherichia coli FVEC1302]
 gi|300308326|gb|EFJ62846.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 200-1]
 gi|300355153|gb|EFJ71023.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 198-1]
 gi|300397877|gb|EFJ81415.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 69-1]
 gi|300415349|gb|EFJ98659.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 115-1]
 gi|300420000|gb|EFK03311.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 182-1]
 gi|300457482|gb|EFK20975.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 21-1]
 gi|300525801|gb|EFK46870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 119-7]
 gi|300528620|gb|EFK49682.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 107-1]
 gi|306909203|gb|EFN39698.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W]
 gi|308122590|gb|EFO59852.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 145-7]
 gi|312286807|gb|EFR14718.1| RNA polymerase sigma factor rpoD [Escherichia coli 2362-75]
 gi|313648184|gb|EFS12630.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2a str. 2457T]
 gi|315062375|gb|ADT76702.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli W]
 gi|320176471|gb|EFW51521.1| RNA polymerase sigma factor RpoD [Shigella dysenteriae CDC 74-1112]
 gi|320179315|gb|EFW54273.1| RNA polymerase sigma factor RpoD [Shigella boydii ATCC 9905]
 gi|320182888|gb|EFW57762.1| RNA polymerase sigma factor RpoD [Shigella flexneri CDC 796-83]
 gi|320189419|gb|EFW64078.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            EC1212]
 gi|320201978|gb|EFW76553.1| RNA polymerase sigma factor RpoD [Escherichia coli EC4100B]
 gi|320640141|gb|EFX09713.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            G5101]
 gi|320645439|gb|EFX14448.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str.
            493-89]
 gi|320650750|gb|EFX19207.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H- str. H
            2687]
 gi|320656128|gb|EFX24040.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            3256-97 TW 07815]
 gi|320661818|gb|EFX29226.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str. USDA
            5905]
 gi|320666969|gb|EFX33945.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str.
            LSU-61]
 gi|323154524|gb|EFZ40724.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa14]
 gi|323163118|gb|EFZ48951.1| RNA polymerase sigma factor rpoD [Escherichia coli E128010]
 gi|323168088|gb|EFZ53775.1| RNA polymerase sigma factor rpoD [Shigella sonnei 53G]
 gi|323173687|gb|EFZ59316.1| RNA polymerase sigma factor rpoD [Escherichia coli LT-68]
 gi|323178773|gb|EFZ64349.1| RNA polymerase sigma factor rpoD [Escherichia coli OK1180]
 gi|323183651|gb|EFZ69048.1| RNA polymerase sigma factor rpoD [Escherichia coli OK1357]
 gi|323188489|gb|EFZ73774.1| RNA polymerase sigma factor rpoD [Escherichia coli RN587/1]
 gi|323377037|gb|ADX49305.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli KO11FL]
 gi|323946863|gb|EGB42881.1| RNA polymerase sigma protein RpoD [Escherichia coli H120]
 gi|323966596|gb|EGB62029.1| RNA polymerase sigma proteinRpoD [Escherichia coli M863]
 gi|323978859|gb|EGB73939.1| RNA polymerase sigma proteinRpoD [Escherichia coli TW10509]
 gi|324011983|gb|EGB81202.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 60-1]
 gi|324018214|gb|EGB87433.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 117-3]
 gi|324119675|gb|EGC13556.1| RNA polymerase sigma proteinRpoD [Escherichia coli E1167]
 gi|326337771|gb|EGD61605.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str. 1125]
 gi|326347336|gb|EGD71061.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 str. 1044]
 gi|327251853|gb|EGE63539.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_7v]
 gi|331048049|gb|EGI20126.1| RNA polymerase sigma factor RpoD [Escherichia coli M718]
 gi|331058611|gb|EGI30592.1| RNA polymerase sigma factor RpoD [Escherichia coli TA143]
 gi|331062821|gb|EGI34735.1| RNA polymerase sigma factor RpoD [Escherichia coli TA271]
 gi|331073208|gb|EGI44531.1| RNA polymerase sigma factor RpoD [Escherichia coli H591]
 gi|331078335|gb|EGI49541.1| RNA polymerase sigma factor RpoD [Escherichia coli H299]
 gi|332086727|gb|EGI91867.1| RNA polymerase sigma factor rpoD [Shigella boydii 5216-82]
 gi|332086765|gb|EGI91902.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332086940|gb|EGI92075.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 155-74]
 gi|332092163|gb|EGI97241.1| RNA polymerase sigma factor rpoD [Shigella boydii 3594-74]
 gi|332102466|gb|EGJ05812.1| RNA polymerase sigma 70 (sigma D) factor [Shigella sp. D9]
 gi|332752740|gb|EGJ83125.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-671]
 gi|332753124|gb|EGJ83508.1| RNA polymerase sigma factor rpoD [Shigella flexneri 4343-70]
 gi|332754402|gb|EGJ84768.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2747-71]
 gi|332765316|gb|EGJ95540.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 2930-71]
 gi|332998670|gb|EGK18266.1| RNA polymerase sigma factor rpoD [Shigella flexneri VA-6]
 gi|332999827|gb|EGK19411.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-272]
 gi|332999919|gb|EGK19502.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-218]
 gi|333014798|gb|EGK34143.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-304]
 gi|333015695|gb|EGK35034.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-227]
 gi|335573942|gb|EGM60280.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri J1713]
 gi|338768857|gb|EGP23645.1| RNA polymerase sigma factor rpoD [Escherichia coli PCN033]
 gi|340732594|gb|EGR61730.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            01-09591]
 gi|341919169|gb|EGT68781.1| hypothetical protein C22711_2811 [Escherichia coli O104:H4 str.
            C227-11]
 gi|342929693|gb|EGU98415.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 79-10]
 gi|345333067|gb|EGW65519.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_C165-02]
 gi|345334573|gb|EGW67016.1| RNA polymerase sigma factor rpoD [Escherichia coli 2534-86]
 gi|345336137|gb|EGW68574.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_B2F1]
 gi|345348377|gb|EGW80671.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_94C]
 gi|345351050|gb|EGW83324.1| RNA polymerase sigma factor rpoD [Escherichia coli 3030-1]
 gi|345356206|gb|EGW88413.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_DG131-3]
 gi|345370923|gb|EGX02897.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_MHI813]
 gi|345375125|gb|EGX07074.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_H.1.8]
 gi|349739612|gb|AEQ14318.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli O7:K1
            str. CE10]
 gi|354860431|gb|EHF20877.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            C236-11]
 gi|354863749|gb|EHF24180.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            C227-11]
 gi|354866039|gb|EHF26463.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            04-8351]
 gi|354872496|gb|EHF32886.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            09-7901]
 gi|354878430|gb|EHF38779.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-3677]
 gi|354887660|gb|EHF47933.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4404]
 gi|354891372|gb|EHF51602.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4522]
 gi|354895993|gb|EHF56171.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4623]
 gi|354907345|gb|EHF67409.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C1]
 gi|354909785|gb|EHF69815.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C2]
 gi|354913209|gb|EHF73205.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C3]
 gi|354915567|gb|EHF75544.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C4]
 gi|354922672|gb|EHF82586.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-4632 C5]
 gi|371594640|gb|EHN83502.1| RNA polymerase sigma factor rpoD [Escherichia coli H494]
 gi|371601030|gb|EHN89799.1| RNA polymerase sigma factor rpoD [Escherichia coli TA124]
 gi|371606439|gb|EHN95036.1| RNA polymerase sigma factor rpoD [Escherichia coli E101]
 gi|371609641|gb|EHN98176.1| RNA polymerase sigma factor rpoD [Escherichia coli B093]
 gi|373246580|gb|EHP66033.1| RNA polymerase sigma factor rpoD [Escherichia coli 4_1_47FAA]
 gi|374360468|gb|AEZ42175.1| RNA polymerase sigma factor RpoD [Escherichia coli O55:H7 str.
            RM12579]
 gi|375320749|gb|EHS66665.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H43 str. T22]
 gi|377841039|gb|EHU06106.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1A]
 gi|377841310|gb|EHU06376.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1C]
 gi|377844478|gb|EHU09514.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1B]
 gi|377854593|gb|EHU19470.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC1D]
 gi|377857792|gb|EHU22640.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC1E]
 gi|377861791|gb|EHU26608.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC2A]
 gi|377871725|gb|EHU36383.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2B]
 gi|377874463|gb|EHU39090.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2C]
 gi|377876798|gb|EHU41397.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2D]
 gi|377887031|gb|EHU51509.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC2E]
 gi|377891201|gb|EHU55654.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3A]
 gi|377891687|gb|EHU56139.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3B]
 gi|377903501|gb|EHU67792.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3C]
 gi|377907687|gb|EHU71910.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3D]
 gi|377909557|gb|EHU73757.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3E]
 gi|377919409|gb|EHU83452.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC3F]
 gi|377924369|gb|EHU88316.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4A]
 gi|377928635|gb|EHU92545.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4B]
 gi|377939685|gb|EHV03439.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4D]
 gi|377940990|gb|EHV04736.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4C]
 gi|377945817|gb|EHV09507.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4E]
 gi|377955772|gb|EHV19326.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC4F]
 gi|377958422|gb|EHV21935.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5A]
 gi|377963293|gb|EHV26740.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5B]
 gi|377971622|gb|EHV34976.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5C]
 gi|377973358|gb|EHV36699.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC5D]
 gi|378030724|gb|EHV93317.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7B]
 gi|378044733|gb|EHW07145.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC8A]
 gi|378045265|gb|EHW07665.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8B]
 gi|378050706|gb|EHW13033.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8C]
 gi|378059972|gb|EHW22171.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8D]
 gi|378063400|gb|EHW25569.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC8E]
 gi|378070980|gb|EHW33053.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9A]
 gi|378075370|gb|EHW37394.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9B]
 gi|378081696|gb|EHW43646.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9C]
 gi|378088088|gb|EHW49943.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9D]
 gi|378092424|gb|EHW54250.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC9E]
 gi|378103892|gb|EHW65555.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10B]
 gi|378109200|gb|EHW70811.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10C]
 gi|378125682|gb|EHW87080.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10E]
 gi|378127514|gb|EHW88903.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC11A]
 gi|378139679|gb|EHX00911.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC11B]
 gi|378146225|gb|EHX07378.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11D]
 gi|378148680|gb|EHX09817.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11C]
 gi|378156108|gb|EHX17160.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC11E]
 gi|378162814|gb|EHX23771.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12B]
 gi|378167117|gb|EHX28034.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC12A]
 gi|378167452|gb|EHX28364.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC12C]
 gi|378180314|gb|EHX41006.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12D]
 gi|378184757|gb|EHX45393.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13A]
 gi|378185179|gb|EHX45810.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC12E]
 gi|378197655|gb|EHX58132.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13C]
 gi|378198052|gb|EHX58525.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13B]
 gi|378201218|gb|EHX61667.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13D]
 gi|378210816|gb|EHX71166.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC13E]
 gi|378214346|gb|EHX74653.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC14A]
 gi|378217037|gb|EHX77318.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14B]
 gi|378226027|gb|EHX86220.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14C]
 gi|378229570|gb|EHX89707.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC14D]
 gi|378236182|gb|EHX96237.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15A]
 gi|378241254|gb|EHY01221.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15B]
 gi|378245857|gb|EHY05794.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15C]
 gi|378253319|gb|EHY13197.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15D]
 gi|378258076|gb|EHY17911.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC15E]
 gi|383391499|gb|AFH16457.1| RNA polymerase sigma factor RpoD [Escherichia coli KO11FL]
 gi|383406663|gb|AFH12906.1| RNA polymerase sigma factor RpoD [Escherichia coli W]
 gi|383468391|gb|EID63412.1| RNA polymerase sigma factor RpoD [Shigella flexneri 5a str. M90T]
 gi|383476006|gb|EID67957.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli W26]
 gi|384471187|gb|EIE55272.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli AI27]
 gi|385710406|gb|EIG47397.1| RNA polymerase sigma factor rpoD [Escherichia coli B799]
 gi|386139763|gb|EIG80918.1| RNA polymerase sigma factor RpoD [Escherichia coli 1.2741]
 gi|386146785|gb|EIG93230.1| RNA polymerase sigma factor RpoD [Escherichia coli 97.0246]
 gi|386151614|gb|EIH02903.1| RNA polymerase sigma factor RpoD [Escherichia coli 5.0588]
 gi|386154557|gb|EIH10918.1| RNA polymerase sigma factor RpoD [Escherichia coli 97.0259]
 gi|386162855|gb|EIH24651.1| RNA polymerase sigma factor RpoD [Escherichia coli 1.2264]
 gi|386166132|gb|EIH32652.1| RNA polymerase sigma factor RpoD [Escherichia coli 96.0497]
 gi|386177990|gb|EIH55469.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.2608]
 gi|386182525|gb|EIH65283.1| RNA polymerase sigma factor RpoD [Escherichia coli 93.0624]
 gi|386187398|gb|EIH76218.1| RNA polymerase sigma factor RpoD [Escherichia coli 4.0522]
 gi|386195589|gb|EIH89824.1| RNA polymerase sigma factor RpoD [Escherichia coli JB1-95]
 gi|386202245|gb|EII01236.1| RNA polymerase sigma factor RpoD [Escherichia coli 96.154]
 gi|386207534|gb|EII12039.1| RNA polymerase sigma factor RpoD [Escherichia coli 5.0959]
 gi|386210522|gb|EII20996.1| RNA polymerase sigma factor RpoD [Escherichia coli 9.0111]
 gi|386219551|gb|EII36015.1| RNA polymerase sigma factor RpoD [Escherichia coli 4.0967]
 gi|386230170|gb|EII57525.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.3884]
 gi|386245748|gb|EII87478.1| RNA polymerase sigma factor RpoD [Escherichia coli 3003]
 gi|386259834|gb|EIJ15308.1| RNA polymerase sigma factor RpoD [Escherichia coli 900105 (10e)]
 gi|386797713|gb|AFJ30747.1| RNA polymerase sigma factor RpoD [Escherichia coli Xuzhou21]
 gi|388336555|gb|EIL03094.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9534]
 gi|388338057|gb|EIL04537.1| RNA polymerase sigma factor RpoD [Escherichia coli O103:H2 str.
            CVM9450]
 gi|388340327|gb|EIL06573.1| RNA polymerase sigma factor RpoD [Escherichia coli O103:H25 str.
            CVM9340]
 gi|388348949|gb|EIL14507.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9570]
 gi|388350380|gb|EIL15770.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9545]
 gi|388358453|gb|EIL22902.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9574]
 gi|388370710|gb|EIL34224.1| hypothetical protein ECO10026_27460 [Escherichia coli O26:H11 str.
            CVM10026]
 gi|388380749|gb|EIL43334.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM9942]
 gi|388386789|gb|EIL48428.1| RNA polymerase sigma factor RpoD [Escherichia coli KD2]
 gi|388391307|gb|EIL52777.1| RNA polymerase sigma factor RpoD [Escherichia coli 541-15]
 gi|388405636|gb|EIL66060.1| RNA polymerase sigma factor RpoD [Escherichia coli 576-1]
 gi|388407465|gb|EIL67836.1| RNA polymerase sigma factor RpoD [Escherichia coli 541-1]
 gi|388421980|gb|EIL81575.1| RNA polymerase sigma factor RpoD [Escherichia coli CUMT8]
 gi|390639272|gb|EIN18751.1| RNA polymerase sigma factor [Escherichia coli FRIK1996]
 gi|390640969|gb|EIN20412.1| RNA polymerase sigma factor [Escherichia coli FDA517]
 gi|390641348|gb|EIN20779.1| RNA polymerase sigma factor [Escherichia coli FDA505]
 gi|390658618|gb|EIN36403.1| RNA polymerase sigma factor [Escherichia coli FRIK1985]
 gi|390658783|gb|EIN36567.1| RNA polymerase sigma factor [Escherichia coli 93-001]
 gi|390661837|gb|EIN39486.1| RNA polymerase sigma factor [Escherichia coli FRIK1990]
 gi|390675576|gb|EIN51716.1| RNA polymerase sigma factor [Escherichia coli PA3]
 gi|390679049|gb|EIN54984.1| RNA polymerase sigma factor [Escherichia coli PA5]
 gi|390682551|gb|EIN58311.1| RNA polymerase sigma factor [Escherichia coli PA9]
 gi|390694245|gb|EIN68846.1| RNA polymerase sigma factor [Escherichia coli PA10]
 gi|390698746|gb|EIN73120.1| RNA polymerase sigma factor [Escherichia coli PA14]
 gi|390699181|gb|EIN73540.1| RNA polymerase sigma factor [Escherichia coli PA15]
 gi|390712726|gb|EIN85670.1| RNA polymerase sigma factor [Escherichia coli PA22]
 gi|390719947|gb|EIN92661.1| RNA polymerase sigma factor [Escherichia coli PA25]
 gi|390722002|gb|EIN94692.1| RNA polymerase sigma factor [Escherichia coli PA24]
 gi|390725742|gb|EIN98235.1| RNA polymerase sigma factor [Escherichia coli PA28]
 gi|390739328|gb|EIO10510.1| RNA polymerase sigma factor [Escherichia coli PA31]
 gi|390740124|gb|EIO11274.1| RNA polymerase sigma factor [Escherichia coli PA32]
 gi|390743526|gb|EIO14495.1| RNA polymerase sigma factor [Escherichia coli PA33]
 gi|390756707|gb|EIO26208.1| RNA polymerase sigma factor [Escherichia coli PA40]
 gi|390764401|gb|EIO33612.1| RNA polymerase sigma factor [Escherichia coli PA39]
 gi|390765301|gb|EIO34480.1| RNA polymerase sigma factor [Escherichia coli PA41]
 gi|390767043|gb|EIO36151.1| RNA polymerase sigma factor [Escherichia coli PA42]
 gi|390780192|gb|EIO47892.1| RNA polymerase sigma factor [Escherichia coli TW06591]
 gi|390787536|gb|EIO55015.1| RNA polymerase sigma factor [Escherichia coli TW07945]
 gi|390789032|gb|EIO56497.1| RNA polymerase sigma factor [Escherichia coli TW10246]
 gi|390794638|gb|EIO61928.1| RNA polymerase sigma factor [Escherichia coli TW11039]
 gi|390803062|gb|EIO70090.1| RNA polymerase sigma factor [Escherichia coli TW09098]
 gi|390805655|gb|EIO72591.1| RNA polymerase sigma factor [Escherichia coli TW09109]
 gi|390814583|gb|EIO81147.1| RNA polymerase sigma factor [Escherichia coli TW10119]
 gi|390824060|gb|EIO90065.1| RNA polymerase sigma factor [Escherichia coli EC4203]
 gi|390826403|gb|EIO92250.1| RNA polymerase sigma factor [Escherichia coli TW09195]
 gi|390829015|gb|EIO94641.1| RNA polymerase sigma factor [Escherichia coli EC4196]
 gi|390843536|gb|EIP07327.1| RNA polymerase sigma factor [Escherichia coli TW14313]
 gi|390844394|gb|EIP08131.1| RNA polymerase sigma factor [Escherichia coli TW14301]
 gi|390849161|gb|EIP12607.1| RNA polymerase sigma factor [Escherichia coli EC4421]
 gi|390859526|gb|EIP21872.1| RNA polymerase sigma factor [Escherichia coli EC4422]
 gi|390864069|gb|EIP26197.1| RNA polymerase sigma factor [Escherichia coli EC4013]
 gi|390868655|gb|EIP30392.1| RNA polymerase sigma factor [Escherichia coli EC4402]
 gi|390876698|gb|EIP37674.1| RNA polymerase sigma factor [Escherichia coli EC4439]
 gi|390882340|gb|EIP42881.1| RNA polymerase sigma factor [Escherichia coli EC4436]
 gi|390891905|gb|EIP51521.1| RNA polymerase sigma factor [Escherichia coli EC4437]
 gi|390894087|gb|EIP53620.1| RNA polymerase sigma factor [Escherichia coli EC4448]
 gi|390898827|gb|EIP58088.1| RNA polymerase sigma factor [Escherichia coli EC1738]
 gi|390907377|gb|EIP66246.1| RNA polymerase sigma factor [Escherichia coli EC1734]
 gi|390917079|gb|EIP75512.1| RNA polymerase sigma factor [Escherichia coli EC1863]
 gi|390918448|gb|EIP76847.1| RNA polymerase sigma factor [Escherichia coli EC1845]
 gi|391246437|gb|EIQ05698.1| RNA polymerase sigma factor rpoD [Shigella flexneri 2850-71]
 gi|391247846|gb|EIQ07091.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-1770]
 gi|391249092|gb|EIQ08329.1| RNA polymerase sigma factor rpoD [Shigella flexneri CCH060]
 gi|391259604|gb|EIQ18678.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-315]
 gi|391263720|gb|EIQ22720.1| RNA polymerase sigma factor rpoD [Shigella flexneri K-404]
 gi|391277630|gb|EIQ36365.1| RNA polymerase sigma factor rpoD [Shigella boydii 4444-74]
 gi|391279540|gb|EIQ38228.1| RNA polymerase sigma factor rpoD [Shigella sonnei 3226-85]
 gi|391282830|gb|EIQ41459.1| RNA polymerase sigma factor rpoD [Shigella sonnei 3233-85]
 gi|391292618|gb|EIQ50939.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            sonnei 4822-66]
 gi|391299495|gb|EIQ57459.1| RNA polymerase sigma factor rpoD [Shigella dysenteriae 225-75]
 gi|391310850|gb|EIQ68500.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli EPEC C342-62]
 gi|394381242|gb|EJE58938.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9602]
 gi|394385497|gb|EJE63027.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10224]
 gi|394389315|gb|EJE66462.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CVM9634]
 gi|394399678|gb|EJE75677.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9553]
 gi|394404581|gb|EJE79941.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10021]
 gi|394409919|gb|EJE84369.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CVM9455]
 gi|394421704|gb|EJE95158.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM9952]
 gi|394432872|gb|EJF04935.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CVM10030]
 gi|397783796|gb|EJK94653.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_O31]
 gi|397895420|gb|EJL11849.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 6603-63]
 gi|397896756|gb|EJL13169.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            sonnei str. Moseley]
 gi|404337161|gb|EJZ63616.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Shigella
            flexneri 1485-80]
 gi|406776026|gb|AFS55450.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2009EL-2050]
 gi|407052601|gb|AFS72652.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2011C-3493]
 gi|407067074|gb|AFS88121.1| RNA polymerase sigma factor RpoD [Escherichia coli O104:H4 str.
            2009EL-2071]
 gi|408062994|gb|EKG97493.1| RNA polymerase sigma factor [Escherichia coli PA7]
 gi|408065209|gb|EKG99684.1| RNA polymerase sigma factor [Escherichia coli FRIK920]
 gi|408068294|gb|EKH02719.1| RNA polymerase sigma factor [Escherichia coli PA34]
 gi|408077797|gb|EKH11988.1| RNA polymerase sigma factor [Escherichia coli FDA506]
 gi|408081283|gb|EKH15305.1| RNA polymerase sigma factor [Escherichia coli FDA507]
 gi|408089808|gb|EKH23101.1| RNA polymerase sigma factor [Escherichia coli FDA504]
 gi|408096050|gb|EKH29006.1| RNA polymerase sigma factor [Escherichia coli FRIK1999]
 gi|408102553|gb|EKH34954.1| RNA polymerase sigma factor [Escherichia coli FRIK1997]
 gi|408107226|gb|EKH39312.1| RNA polymerase sigma factor [Escherichia coli NE1487]
 gi|408113709|gb|EKH45290.1| RNA polymerase sigma factor [Escherichia coli NE037]
 gi|408119779|gb|EKH50829.1| RNA polymerase sigma factor [Escherichia coli FRIK2001]
 gi|408125911|gb|EKH56492.1| RNA polymerase sigma factor [Escherichia coli PA4]
 gi|408136085|gb|EKH65842.1| RNA polymerase sigma factor [Escherichia coli PA23]
 gi|408138629|gb|EKH68286.1| RNA polymerase sigma factor [Escherichia coli PA49]
 gi|408145010|gb|EKH74214.1| RNA polymerase sigma factor [Escherichia coli PA45]
 gi|408153525|gb|EKH81919.1| RNA polymerase sigma factor [Escherichia coli TT12B]
 gi|408158412|gb|EKH86530.1| RNA polymerase sigma factor [Escherichia coli MA6]
 gi|408162436|gb|EKH90342.1| RNA polymerase sigma factor [Escherichia coli 5905]
 gi|408171700|gb|EKH98801.1| RNA polymerase sigma factor [Escherichia coli CB7326]
 gi|408178513|gb|EKI05220.1| RNA polymerase sigma factor [Escherichia coli EC96038]
 gi|408181723|gb|EKI08270.1| RNA polymerase sigma factor [Escherichia coli 5412]
 gi|408199287|gb|EKI24492.1| RNA polymerase sigma factor [Escherichia coli ARS4.2123]
 gi|408215380|gb|EKI39778.1| RNA polymerase sigma factor [Escherichia coli PA38]
 gi|408225369|gb|EKI49051.1| RNA polymerase sigma factor [Escherichia coli EC1735]
 gi|408236629|gb|EKI59522.1| RNA polymerase sigma factor [Escherichia coli EC1736]
 gi|408240247|gb|EKI62952.1| RNA polymerase sigma factor [Escherichia coli EC1737]
 gi|408244820|gb|EKI67230.1| RNA polymerase sigma factor [Escherichia coli EC1846]
 gi|408253758|gb|EKI75345.1| RNA polymerase sigma factor [Escherichia coli EC1847]
 gi|408257514|gb|EKI78828.1| RNA polymerase sigma factor [Escherichia coli EC1848]
 gi|408264050|gb|EKI84866.1| RNA polymerase sigma factor [Escherichia coli EC1849]
 gi|408272710|gb|EKI92785.1| RNA polymerase sigma factor [Escherichia coli EC1850]
 gi|408275598|gb|EKI95554.1| RNA polymerase sigma factor [Escherichia coli EC1856]
 gi|408283922|gb|EKJ03052.1| RNA polymerase sigma factor [Escherichia coli EC1862]
 gi|408289862|gb|EKJ08608.1| RNA polymerase sigma factor [Escherichia coli EC1864]
 gi|408294733|gb|EKJ13105.1| RNA polymerase sigma factor [Escherichia coli EC1865]
 gi|408305642|gb|EKJ23033.1| RNA polymerase sigma factor [Escherichia coli EC1868]
 gi|408306242|gb|EKJ23617.1| RNA polymerase sigma factor [Escherichia coli EC1866]
 gi|408317134|gb|EKJ33377.1| RNA polymerase sigma factor [Escherichia coli EC1869]
 gi|408322760|gb|EKJ38736.1| RNA polymerase sigma factor [Escherichia coli EC1870]
 gi|408325084|gb|EKJ40989.1| RNA polymerase sigma factor [Escherichia coli NE098]
 gi|408335150|gb|EKJ50004.1| RNA polymerase sigma factor [Escherichia coli FRIK523]
 gi|408342085|gb|EKJ56520.1| RNA polymerase sigma factor [Escherichia coli 0.1288]
 gi|408344634|gb|EKJ58989.1| RNA polymerase sigma factor [Escherichia coli 0.1304]
 gi|408547526|gb|EKK24920.1| RNA polymerase sigma factor rpoD [Escherichia coli 5.2239]
 gi|408547765|gb|EKK25158.1| RNA polymerase sigma factor rpoD [Escherichia coli 3.4870]
 gi|408548905|gb|EKK26277.1| RNA polymerase sigma factor [Escherichia coli 6.0172]
 gi|408566337|gb|EKK42410.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.0586]
 gi|408577265|gb|EKK52840.1| RNA polymerase sigma factor [Escherichia coli 10.0833]
 gi|408580118|gb|EKK55556.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.2524]
 gi|408589847|gb|EKK64348.1| RNA polymerase sigma factor rpoD [Escherichia coli 10.0869]
 gi|408595261|gb|EKK69519.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.0221]
 gi|408599828|gb|EKK73711.1| RNA polymerase sigma factor [Escherichia coli 8.0416]
 gi|408610634|gb|EKK84000.1| RNA polymerase sigma factor rpoD [Escherichia coli 10.0821]
 gi|421943861|gb|EKU01133.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H8 str.
            CFSAN001632]
 gi|421948221|gb|EKU05258.1| RNA polymerase sigma factor RpoD [Escherichia coli O26:H11 str.
            CFSAN001629]
 gi|421949087|gb|EKU06079.1| RNA polymerase sigma factor RpoD [Escherichia coli O111:H11 str.
            CFSAN001630]
 gi|427202761|gb|EKV73076.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.1042]
 gi|427204035|gb|EKV74323.1| RNA polymerase sigma factor rpoD [Escherichia coli 89.0511]
 gi|427206601|gb|EKV76805.1| RNA polymerase sigma factor rpoD [Escherichia coli 88.1467]
 gi|427219075|gb|EKV88045.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.0091]
 gi|427222576|gb|EKV91348.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.2281]
 gi|427225837|gb|EKV94454.1| RNA polymerase sigma factor rpoD [Escherichia coli 90.0039]
 gi|427239897|gb|EKW07365.1| RNA polymerase sigma factor rpoD [Escherichia coli 93.0056]
 gi|427240189|gb|EKW07648.1| RNA polymerase sigma factor rpoD [Escherichia coli 93.0055]
 gi|427244179|gb|EKW11514.1| RNA polymerase sigma factor rpoD [Escherichia coli 94.0618]
 gi|427258728|gb|EKW24810.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0183]
 gi|427259587|gb|EKW25623.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0943]
 gi|427262064|gb|EKW27970.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.1288]
 gi|427274907|gb|EKW39544.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0428]
 gi|427277613|gb|EKW42146.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0427]
 gi|427281803|gb|EKW46103.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0939]
 gi|427290249|gb|EKW53739.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0932]
 gi|427297350|gb|EKW60387.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0107]
 gi|427299086|gb|EKW62075.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0003]
 gi|427310282|gb|EKW72540.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.1742]
 gi|427313228|gb|EKW75352.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0007]
 gi|427317677|gb|EKW79571.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0672]
 gi|427326020|gb|EKW87446.1| RNA polymerase sigma factor [Escherichia coli 99.0678]
 gi|427327719|gb|EKW89102.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0713]
 gi|429252163|gb|EKY36714.1| RNA polymerase sigma factor rpoD [Escherichia coli 96.0109]
 gi|429253664|gb|EKY38145.1| RNA polymerase sigma factor rpoD [Escherichia coli 97.0010]
 gi|429346478|gb|EKY83257.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02092]
 gi|429357332|gb|EKY94005.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02030]
 gi|429358838|gb|EKY95505.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02033-1]
 gi|429372624|gb|EKZ09173.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02093]
 gi|429374565|gb|EKZ11104.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02281]
 gi|429378247|gb|EKZ14761.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02318]
 gi|429388427|gb|EKZ24852.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-02913]
 gi|429391814|gb|EKZ28217.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-03439]
 gi|429392205|gb|EKZ28606.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-03943]
 gi|429402694|gb|EKZ38984.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            11-04080]
 gi|429404233|gb|EKZ40511.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9990]
 gi|429407944|gb|EKZ44191.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9450]
 gi|429415514|gb|EKZ51679.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4984]
 gi|429419035|gb|EKZ55174.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4986]
 gi|429425389|gb|EKZ61479.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4987]
 gi|429430432|gb|EKZ66497.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-4988]
 gi|429434426|gb|EKZ70453.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-5603]
 gi|429436906|gb|EKZ72921.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-6006]
 gi|429441495|gb|EKZ77465.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-5604]
 gi|429445798|gb|EKZ81737.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec12-0465]
 gi|429455563|gb|EKZ91418.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec12-0466]
 gi|429459278|gb|EKZ95097.1| RNA polymerase sigma factor rpoD [Escherichia coli O104:H4 str.
            Ec11-9941]
 gi|430915348|gb|ELC36427.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE21]
 gi|430923841|gb|ELC44574.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE26]
 gi|430953110|gb|ELC72023.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE181]
 gi|430978598|gb|ELC95409.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE193]
 gi|430986350|gb|ELD02921.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE204]
 gi|430996212|gb|ELD12498.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE206]
 gi|431002641|gb|ELD18148.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE208]
 gi|431004906|gb|ELD20115.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE210]
 gi|431018908|gb|ELD32338.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE213]
 gi|431048513|gb|ELD58489.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE228]
 gi|431058763|gb|ELD68150.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE234]
 gi|431061520|gb|ELD70827.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE233]
 gi|431072162|gb|ELD79914.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE236]
 gi|431077916|gb|ELD84975.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE237]
 gi|431138214|gb|ELE40050.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE66]
 gi|431152084|gb|ELE53042.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE75]
 gi|431168081|gb|ELE68335.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE80]
 gi|431179385|gb|ELE79291.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE83]
 gi|431212188|gb|ELF10130.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE142]
 gi|431218290|gb|ELF15770.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE143]
 gi|431253786|gb|ELF47264.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE8]
 gi|431261037|gb|ELF53128.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE9]
 gi|431294721|gb|ELF84900.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE29]
 gi|431308489|gb|ELF96769.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE48]
 gi|431316325|gb|ELG04135.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE54]
 gi|431322611|gb|ELG10196.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE50]
 gi|431338369|gb|ELG25456.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE78]
 gi|431349954|gb|ELG36782.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE79]
 gi|431353775|gb|ELG40528.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE91]
 gi|431361132|gb|ELG47731.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE101]
 gi|431361853|gb|ELG48432.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE115]
 gi|431383561|gb|ELG67685.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE135]
 gi|431384084|gb|ELG68207.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE136]
 gi|431387516|gb|ELG71340.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE140]
 gi|431398638|gb|ELG82058.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE144]
 gi|431402746|gb|ELG86051.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE146]
 gi|431409509|gb|ELG92684.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE147]
 gi|431414836|gb|ELG97387.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE158]
 gi|431436735|gb|ELH18249.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE190]
 gi|431451272|gb|ELH31748.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE184]
 gi|431455773|gb|ELH36128.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE196]
 gi|431468848|gb|ELH48781.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE203]
 gi|431472108|gb|ELH52000.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE202]
 gi|431528543|gb|ELI05250.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE105]
 gi|431548238|gb|ELI22525.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE112]
 gi|431554364|gb|ELI28245.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE117]
 gi|431562897|gb|ELI36140.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE120]
 gi|431579229|gb|ELI51813.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE125]
 gi|431580450|gb|ELI53009.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE128]
 gi|431594470|gb|ELI64750.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE131]
 gi|431608737|gb|ELI78079.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE138]
 gi|431674970|gb|ELJ41116.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE177]
 gi|431698973|gb|ELJ63994.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE82]
 gi|431713823|gb|ELJ78031.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE90]
 gi|431718222|gb|ELJ82303.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE95]
 gi|441606608|emb|CCP99465.1| RNA polymerase sigma factor RpoD [Escherichia coli O10:K5(L):H4 str.
            ATCC 23506]
 gi|444536382|gb|ELV16406.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0814]
 gi|444538076|gb|ELV17975.1| RNA polymerase sigma factor rpoD [Escherichia coli 09BKT078844]
 gi|444546423|gb|ELV25163.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0815]
 gi|444556022|gb|ELV33455.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0839]
 gi|444556325|gb|ELV33743.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0816]
 gi|444561306|gb|ELV38431.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0848]
 gi|444570714|gb|ELV47231.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1753]
 gi|444574469|gb|ELV50767.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1775]
 gi|444577853|gb|ELV53956.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1793]
 gi|444591129|gb|ELV66421.1| RNA polymerase sigma factor rpoD [Escherichia coli PA11]
 gi|444591227|gb|ELV66518.1| RNA polymerase sigma factor rpoD [Escherichia coli ATCC 700728]
 gi|444592613|gb|ELV67865.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1805]
 gi|444604485|gb|ELV79150.1| RNA polymerase sigma factor rpoD [Escherichia coli PA13]
 gi|444605534|gb|ELV80175.1| RNA polymerase sigma factor rpoD [Escherichia coli PA19]
 gi|444613674|gb|ELV87924.1| RNA polymerase sigma factor rpoD [Escherichia coli PA2]
 gi|444621351|gb|ELV95327.1| RNA polymerase sigma factor rpoD [Escherichia coli PA47]
 gi|444622364|gb|ELV96325.1| RNA polymerase sigma factor rpoD [Escherichia coli PA48]
 gi|444628182|gb|ELW01926.1| RNA polymerase sigma factor rpoD [Escherichia coli PA8]
 gi|444636588|gb|ELW09979.1| RNA polymerase sigma factor rpoD [Escherichia coli 7.1982]
 gi|444639668|gb|ELW12975.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1781]
 gi|444643564|gb|ELW16711.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.1762]
 gi|444652692|gb|ELW25441.1| RNA polymerase sigma factor rpoD [Escherichia coli PA35]
 gi|444658384|gb|ELW30841.1| RNA polymerase sigma factor rpoD [Escherichia coli 3.4880]
 gi|444661438|gb|ELW33750.1| RNA polymerase sigma factor rpoD [Escherichia coli 95.0083]
 gi|444668519|gb|ELW40532.1| RNA polymerase sigma factor rpoD [Escherichia coli 99.0670]
 gi|449311797|gb|EMD02121.1| RNA polymerase sigma factor RpoD [Escherichia coli SEPT362]
 gi|449315181|gb|EMD05329.1| RNA polymerase sigma factor RpoD [Escherichia coli O08]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|119944095|ref|YP_941775.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
 gi|119862699|gb|ABM02176.1| RNA polymerase, sigma 70 subunit, RpoD [Psychromonas ingrahamii 37]
          Length = 617

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 305/623 (48%), Positives = 410/623 (65%), Gaps = 36/623 (5%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K LI  GKE+G+LT++E+ND LP+DI++ E IE II+    M I V E   D + +
Sbjct: 6    QSQLKELIIKGKEKGFLTYAEVNDHLPQDIVESEQIEDIIQMIGDMGIRVVETAPDADDM 65

Query: 890  MLS---NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            ++    + T D+D  EA    L+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 66   LIGADDSETPDEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKR 125

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEG+K++  A+S  P TI  +L   D     E+K+ +++ G +D N            +
Sbjct: 126  IEEGIKEVQTAVSEYPATISGLLDNWDSYEAEEMKLTDLISGFVDPN------------D 173

Query: 1007 NNEEKILIESSSADLSTEQLEKLKY---------------------ESLIKFSNISFHFD 1045
            +  + +      ++LS +QLE                         E+  KF+ +     
Sbjct: 174  DMTQAVSATHIGSELSKKQLEDEDKADKDDSDEDDEEEGPKGPDPEEAAEKFAELRKLNQ 233

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
             +  +  K G        A N  +      +   K  +++   +R  +N V   E+  L+
Sbjct: 234  VVEDSITKNGRAHAETRAAINEQAEFFQQFKLIPKQFDRMVKAIRFAMNAVRVQERLALK 293

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            I V +C MP+  FIK+F  NE N  W++       DY   +      ++   +K++ ++ 
Sbjct: 294  ICVEQCKMPKKEFIKLFKGNETNPAWLEVILSNGTDYATRISEFEEDLRRCLRKMLAVEV 353

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
              VL + +++ I+R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 354  QSVLTITNMKGISRNMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 413

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ
Sbjct: 414  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQ 473

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G EP P  +A +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 474  MLQEMGREPQPEELAERMMMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIA 533

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P++ A + S+++   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 534  LPANCATSESLKNATNDVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 593

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR  +L+ FL+
Sbjct: 594  IEAKALRKLRHPSRSEQLRSFLD 616



 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 298/610 (48%), Positives = 400/610 (65%), Gaps = 36/610 (5%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K LI  GKE+G+LT++E+ND LP+DI++ E IE II+    M I V E   D + +
Sbjct: 6   QSQLKELIIKGKEKGFLTYAEVNDHLPQDIVESEQIEDIIQMIGDMGIRVVETAPDADDM 65

Query: 100 MLS---NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           ++    + T D+D  EA    L+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 66  LIGADDSETPDEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKR 125

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEG+K++  A+S  P TI  +L   D     E+K+ +++ G +D N            +
Sbjct: 126 IEEGIKEVQTAVSEYPATISGLLDNWDSYEAEEMKLTDLISGFVDPN------------D 173

Query: 217 NNEEKILIESSSADLSTEQLEKLKY---------------------ESLIKFSNISFHFD 255
           +  + +      ++LS +QLE                         E+  KF+ +     
Sbjct: 174 DMTQAVSATHIGSELSKKQLEDEDKADKDDSDEDDEEEGPKGPDPEEAAEKFAELRKLNQ 233

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
            +  +  K G        A N  +      +   K  +++   +R  +N V   E+  L+
Sbjct: 234 VVEDSITKNGRAHAETRAAINEQAEFFQQFKLIPKQFDRMVKAIRFAMNAVRVQERLALK 293

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           I V +C MP+  FIK+F  NE N  W++       DY   +      ++   +K++ ++ 
Sbjct: 294 ICVEQCKMPKKEFIKLFKGNETNPAWLEVILSNGTDYATRISEFEEDLRRCLRKMLAVEV 353

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
             VL + +++ I+R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 354 QSVLTITNMKGISRNMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 413

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ
Sbjct: 414 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQ 473

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G EP P  +A +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 474 MLQEMGREPQPEELAERMMMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIA 533

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P++ A + S+++   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 534 LPANCATSESLKNATNDVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 593

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 594 IEAKALRKLR 603


>gi|448824722|dbj|BAM78690.1| RNA polymerase sigma factor, partial [Pseudomonas cannabina pv.
           alisalensis]
          Length = 585

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 304/595 (51%), Positives = 405/595 (68%), Gaps = 28/595 (4%)

Query: 49  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 108
           LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 1   LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 60

Query: 109 DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 168
              E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 61  AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 120

Query: 169 SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGNKNNNEEK 221
           +  P T+  IL    +++    ++ +++ G ID +               K  K   +++
Sbjct: 121 AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDE 180

Query: 222 IL-----------IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
                        +ES    +  +Q          +F  +S   +  RKA +K G + + 
Sbjct: 181 EEETAEATDDEEEVESGPDPVIAQQ----------RFGAVSDQMEITRKALKKFGRDDKH 230

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++
Sbjct: 231 AIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLR 290

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+
Sbjct: 291 QFPGHEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRR 350

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 351 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 410

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 411 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 470

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 471 ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 530

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 531 REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 585



 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 304/595 (51%), Positives = 405/595 (68%), Gaps = 28/595 (4%)

Query: 839  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 898
            LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 1    LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 60

Query: 899  DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 958
               E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 61   AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 120

Query: 959  SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGNKNNNEEK 1011
            +  P T+  IL    +++    ++ +++ G ID +               K  K   +++
Sbjct: 121  AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDE 180

Query: 1012 IL-----------IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
                         +ES    +  +Q          +F  +S   +  RKA +K G + + 
Sbjct: 181  EEETAEATDDEEEVESGPDPVIAQQ----------RFGAVSDQMEITRKALKKFGRDDKH 230

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++
Sbjct: 231  AIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLR 290

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+
Sbjct: 291  QFPGHEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRR 350

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 351  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 410

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 411  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 470

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 471  ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 530

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 531  REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 585


>gi|261820103|ref|YP_003258209.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae WPP163]
 gi|421081028|ref|ZP_15541942.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae CFBP 3304]
 gi|261604116|gb|ACX86602.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium wasabiae
            WPP163]
 gi|401704038|gb|EJS94247.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae CFBP 3304]
          Length = 611

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 308/608 (50%), Positives = 419/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ ++EE    +    +   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183  VGSELSSEEISDDDEEEDEDEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243  AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303  MFTGNETNNSWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 410/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ ++EE    +    +   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183 VGSELSSEEISDDDEEEDEDEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243 AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303 MFTGNETNNSWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|170765503|ref|ZP_02900314.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
 gi|170124649|gb|EDS93580.1| RNA polymerase sigma factor RpoD [Escherichia albertii TW07627]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   +++G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKEKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   +++G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIKEKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|419285944|ref|ZP_13828111.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10F]
 gi|378128943|gb|EHW90323.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10F]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 412/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+  F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKSF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 403/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+  F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKSF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|317049603|ref|YP_004117251.1| RNA polymerase sigma-70 subunit RpoD [Pantoea sp. At-9b]
 gi|316951220|gb|ADU70695.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. At-9b]
          Length = 614

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 307/614 (50%), Positives = 413/614 (67%), Gaps = 15/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 887  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  +  +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLNENSADTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNN----------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 1054
              +           E+    +  S+D       +L  E   KF  +   ++  R   + +
Sbjct: 183  VGSELSEEDRDDDDEDDEESDDDSSDDDNSIDPELARE---KFVELRTQYETTRTVIKAK 239

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +    +    N+S      R   K  + L + +R  + +V   E+ I+++ V  C MP
Sbjct: 240  GRSHADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERIIMKLCVELCKMP 299

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            + +FI +F  NE + +W      +   ++  L      +    QKL+ ++ +  L +  +
Sbjct: 300  KKNFITLFTGNETSESWFKAALAMNKPWSEKLLEVQDDVMRCLQKLLQIEEETGLTIEQV 359

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 360  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 419

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 420  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 479

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 480  TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 539

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 540  SLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 599

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 600  RHPSRSEVLRSFLD 613



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 300/601 (49%), Positives = 404/601 (67%), Gaps = 15/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVVEEAPDA 62

Query: 97  ETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  +  +D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLNENSADTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVEAGESRLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNN----------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 264
             +           E+    +  S+D       +L  E   KF  +   ++  R   + +
Sbjct: 183 VGSELSEEDRDDDDEDDEESDDDSSDDDNSIDPELARE---KFVELRTQYETTRTVIKAK 239

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +    +    N+S      R   K  + L + +R  + +V   E+ I+++ V  C MP
Sbjct: 240 GRSHADAVAEIQNLSEVFKQFRLVPKQFDYLVNNMREMMERVRTQERIIMKLCVELCKMP 299

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           + +FI +F  NE + +W      +   ++  L      +    QKL+ ++ +  L +  +
Sbjct: 300 KKNFITLFTGNETSESWFKAALAMNKPWSEKLLEVQDDVMRCLQKLLQIEEETGLTIEQV 359

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 360 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 419

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 420 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 479

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 480 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSE 539

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 540 SLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 599

Query: 625 R 625
           R
Sbjct: 600 R 600


>gi|366160075|ref|ZP_09459937.1| RNA polymerase sigma factor RpoD [Escherichia sp. TW09308]
 gi|432373659|ref|ZP_19616693.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE11]
 gi|430894183|gb|ELC16474.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE11]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 412/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDADDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 403/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N          +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEELAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDADDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|359454610|ref|ZP_09243886.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20495]
 gi|414069707|ref|ZP_11405699.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. Bsw20308]
 gi|358048323|dbj|GAA80135.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20495]
 gi|410807937|gb|EKS13911.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. Bsw20308]
          Length = 616

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 320/622 (51%), Positives = 413/622 (66%), Gaps = 36/622 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY-----------------------ESLIKFSNISFHFDKMR 1048
            I   +  ++LS +QL+                           E+ I F N+   ++K R
Sbjct: 175  ISATNIGSELSAKQLDDDDKDDKDDADSDDEDEEEIDTGPDPEEARIHFENLRDLYNKAR 234

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
              FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V
Sbjct: 235  DTFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAV 294

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
                +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    
Sbjct: 295  QIAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTG 354

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 355  LSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 415  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P 
Sbjct: 475  EMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPI 534

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 535  DSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594

Query: 1409 KALRKLRHPSRYYKLKIFLEGK 1430
            KALRKLRHPSR   LK FL+ K
Sbjct: 595  KALRKLRHPSRSDLLKSFLDAK 616



 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 314/615 (51%), Positives = 406/615 (66%), Gaps = 37/615 (6%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 222 ILIESSSADLSTEQLEKLKY-----------------------ESLIKFSNISFHFDKMR 258
           I   +  ++LS +QL+                           E+ I F N+   ++K R
Sbjct: 175 ISATNIGSELSAKQLDDDDKDDKDDADSDDEDEEEIDTGPDPEEARIHFENLRDLYNKAR 234

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
             FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V
Sbjct: 235 DTFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAV 294

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
               +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    
Sbjct: 295 QIAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTG 354

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 355 LSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P 
Sbjct: 475 EMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPI 534

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 535 DSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594

Query: 619 KALRKLR-PLAHDWL 632
           KALRKLR P   D L
Sbjct: 595 KALRKLRHPSRSDLL 609


>gi|332531768|ref|ZP_08407653.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
            ANT/505]
 gi|332038744|gb|EGI75186.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas haloplanktis
            ANT/505]
          Length = 616

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 321/622 (51%), Positives = 413/622 (66%), Gaps = 36/622 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY-----------------------ESLIKFSNISFHFDKMR 1048
            I   +  ++LS +QLE                           E+ I F N+   ++K R
Sbjct: 175  ISATNIGSELSAKQLEDDDKDDKDDADSDDEDEEEIDTGPDPEEARIHFENLRDLYNKAR 234

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
              FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V
Sbjct: 235  DTFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAV 294

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
                +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    
Sbjct: 295  QIAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTG 354

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 355  LSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 415  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P 
Sbjct: 475  EMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPI 534

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 535  DSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594

Query: 1409 KALRKLRHPSRYYKLKIFLEGK 1430
            KALRKLRHPSR   LK FL+ K
Sbjct: 595  KALRKLRHPSRSDLLKSFLDAK 616



 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 315/615 (51%), Positives = 406/615 (66%), Gaps = 37/615 (6%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 222 ILIESSSADLSTEQLEKLKY-----------------------ESLIKFSNISFHFDKMR 258
           I   +  ++LS +QLE                           E+ I F N+   ++K R
Sbjct: 175 ISATNIGSELSAKQLEDDDKDDKDDADSDDEDEEEIDTGPDPEEARIHFENLRDLYNKAR 234

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
             FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V
Sbjct: 235 DTFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRVQERLIMKQAV 294

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
               +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    
Sbjct: 295 QIAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTG 354

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 355 LSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P 
Sbjct: 475 EMGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPI 534

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 535 DSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594

Query: 619 KALRKLR-PLAHDWL 632
           KALRKLR P   D L
Sbjct: 595 KALRKLRHPSRSDLL 609


>gi|91212497|ref|YP_542483.1| RNA polymerase sigma factor RpoD [Escherichia coli UTI89]
 gi|117625379|ref|YP_855524.1| RNA polymerase sigma factor RpoD [Escherichia coli APEC O1]
 gi|218560154|ref|YP_002393067.1| RNA polymerase sigma factor RpoD [Escherichia coli S88]
 gi|218691372|ref|YP_002399584.1| RNA polymerase sigma factor RpoD [Escherichia coli ED1a]
 gi|227887792|ref|ZP_04005597.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|237706170|ref|ZP_04536651.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|300973231|ref|ZP_07172070.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|301048094|ref|ZP_07195132.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|306816579|ref|ZP_07450711.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|331648869|ref|ZP_08349957.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331659358|ref|ZP_08360300.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli TA206]
 gi|386601108|ref|YP_006102614.1| RNA polymerase sigma factor RpoD [Escherichia coli IHE3034]
 gi|386602834|ref|YP_006109134.1| RNA polymerase sigma factor RpoD [Escherichia coli UM146]
 gi|386620694|ref|YP_006140274.1| RNA polymerase sigma factor [Escherichia coli NA114]
 gi|386630954|ref|YP_006150674.1| hypothetical protein i02_3514 [Escherichia coli str. 'clone D i2']
 gi|386635874|ref|YP_006155593.1| hypothetical protein i14_3514 [Escherichia coli str. 'clone D i14']
 gi|386640682|ref|YP_006107480.1| hypothetical protein ECABU_c34860 [Escherichia coli ABU 83972]
 gi|387618377|ref|YP_006121399.1| RNA polymerase sigma factor RpoD [Escherichia coli O83:H1 str. NRG
            857C]
 gi|387830964|ref|YP_003350901.1| RNA polymerase sigma factor RpoD [Escherichia coli SE15]
 gi|416337096|ref|ZP_11673566.1| RNA polymerase sigma factor RpoD [Escherichia coli WV_060327]
 gi|417086779|ref|ZP_11953876.1| RNA polymerase sigma factor RpoD [Escherichia coli cloneA_i1]
 gi|417285873|ref|ZP_12073164.1| RNA polymerase sigma factor RpoD [Escherichia coli TW07793]
 gi|417663660|ref|ZP_12313240.1| RNA polymerase sigma factor RpoD [Escherichia coli AA86]
 gi|419701912|ref|ZP_14229510.1| RNA polymerase sigma factor RpoD [Escherichia coli SCI-07]
 gi|419913409|ref|ZP_14431842.1| RNA polymerase sigma factor RpoD [Escherichia coli KD1]
 gi|419946099|ref|ZP_14462516.1| RNA polymerase sigma factor RpoD [Escherichia coli HM605]
 gi|422357343|ref|ZP_16438010.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 110-3]
 gi|422362240|ref|ZP_16442811.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 153-1]
 gi|422370470|ref|ZP_16450863.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 16-3]
 gi|422379904|ref|ZP_16460085.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 57-2]
 gi|422749816|ref|ZP_16803727.1| RNA polymerase sigma proteinRpoD [Escherichia coli H252]
 gi|422753977|ref|ZP_16807803.1| RNA polymerase sigma proteinRpoD [Escherichia coli H263]
 gi|422841098|ref|ZP_16889068.1| RNA polymerase sigma factor rpoD [Escherichia coli H397]
 gi|425301943|ref|ZP_18691827.1| RNA polymerase sigma factor [Escherichia coli 07798]
 gi|432359538|ref|ZP_19602752.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE4]
 gi|432364335|ref|ZP_19607492.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE5]
 gi|432382811|ref|ZP_19625750.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE15]
 gi|432388842|ref|ZP_19631722.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE16]
 gi|432399034|ref|ZP_19641809.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE25]
 gi|432408160|ref|ZP_19650864.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE28]
 gi|432413310|ref|ZP_19655965.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE39]
 gi|432423494|ref|ZP_19666033.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE178]
 gi|432433302|ref|ZP_19675727.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE187]
 gi|432437897|ref|ZP_19680281.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE188]
 gi|432442574|ref|ZP_19684910.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE189]
 gi|432447694|ref|ZP_19689991.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE191]
 gi|432458210|ref|ZP_19700387.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE201]
 gi|432467394|ref|ZP_19709473.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE205]
 gi|432497203|ref|ZP_19738996.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE214]
 gi|432501643|ref|ZP_19743395.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE216]
 gi|432505960|ref|ZP_19747680.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE220]
 gi|432525415|ref|ZP_19762534.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE230]
 gi|432555149|ref|ZP_19791868.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE47]
 gi|432560352|ref|ZP_19797008.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE49]
 gi|432570312|ref|ZP_19806819.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE53]
 gi|432575285|ref|ZP_19811759.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE55]
 gi|432581725|ref|ZP_19818139.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE57]
 gi|432589469|ref|ZP_19825822.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE58]
 gi|432594283|ref|ZP_19830596.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE60]
 gi|432599337|ref|ZP_19835608.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE62]
 gi|432609123|ref|ZP_19845305.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE67]
 gi|432613092|ref|ZP_19849250.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE72]
 gi|432647760|ref|ZP_19883546.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE86]
 gi|432652681|ref|ZP_19888427.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE87]
 gi|432657323|ref|ZP_19893020.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE93]
 gi|432695953|ref|ZP_19931146.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE162]
 gi|432707430|ref|ZP_19942507.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE6]
 gi|432724553|ref|ZP_19959467.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE17]
 gi|432729134|ref|ZP_19964009.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE18]
 gi|432733841|ref|ZP_19968666.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE45]
 gi|432742823|ref|ZP_19977538.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE23]
 gi|432756019|ref|ZP_19990564.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE22]
 gi|432760927|ref|ZP_19995417.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE46]
 gi|432780099|ref|ZP_20014320.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE59]
 gi|432785055|ref|ZP_20019233.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE63]
 gi|432789092|ref|ZP_20023220.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE65]
 gi|432803260|ref|ZP_20037215.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE84]
 gi|432822527|ref|ZP_20056216.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE118]
 gi|432823982|ref|ZP_20057652.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE123]
 gi|432846131|ref|ZP_20078812.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE141]
 gi|432890455|ref|ZP_20103387.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE165]
 gi|432900311|ref|ZP_20110733.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE192]
 gi|432906730|ref|ZP_20115269.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE194]
 gi|432922101|ref|ZP_20125065.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE173]
 gi|432928900|ref|ZP_20130001.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE175]
 gi|432939709|ref|ZP_20137812.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE183]
 gi|432973361|ref|ZP_20162207.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE207]
 gi|432975290|ref|ZP_20164125.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE209]
 gi|432982532|ref|ZP_20171303.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE211]
 gi|432986935|ref|ZP_20175648.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE215]
 gi|432992187|ref|ZP_20180846.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE217]
 gi|432996850|ref|ZP_20185433.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE218]
 gi|433001446|ref|ZP_20189965.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE223]
 gi|433006670|ref|ZP_20195094.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE227]
 gi|433009286|ref|ZP_20197699.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE229]
 gi|433015363|ref|ZP_20203700.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE104]
 gi|433024930|ref|ZP_20212906.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE106]
 gi|433029998|ref|ZP_20217850.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE109]
 gi|433040078|ref|ZP_20227673.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE113]
 gi|433059545|ref|ZP_20246584.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE124]
 gi|433074333|ref|ZP_20260975.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE129]
 gi|433084003|ref|ZP_20270454.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE133]
 gi|433088739|ref|ZP_20275105.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE137]
 gi|433097888|ref|ZP_20284064.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE139]
 gi|433102664|ref|ZP_20288739.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE145]
 gi|433107336|ref|ZP_20293301.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE148]
 gi|433112319|ref|ZP_20298175.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE150]
 gi|433116965|ref|ZP_20302751.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE153]
 gi|433126626|ref|ZP_20312176.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE160]
 gi|433140693|ref|ZP_20325941.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE167]
 gi|433150721|ref|ZP_20335723.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE174]
 gi|433155235|ref|ZP_20340168.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE176]
 gi|433165077|ref|ZP_20349808.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE179]
 gi|433170053|ref|ZP_20354676.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE180]
 gi|433184796|ref|ZP_20369034.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE85]
 gi|433189865|ref|ZP_20373956.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE88]
 gi|433199808|ref|ZP_20383698.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE94]
 gi|433209187|ref|ZP_20392857.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE97]
 gi|433214036|ref|ZP_20397622.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE99]
 gi|433325614|ref|ZP_20402673.1| RNA polymerase sigma factor RpoD [Escherichia coli J96]
 gi|442605279|ref|ZP_21020111.1| RNA polymerase sigma factor RpoD [Escherichia coli Nissle 1917]
 gi|91074071|gb|ABE08952.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
            high temperatures [Escherichia coli UTI89]
 gi|115514503|gb|ABJ02578.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
            high temperatures [Escherichia coli APEC O1]
 gi|218366923|emb|CAR04694.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli S88]
 gi|218428936|emb|CAR09739.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli ED1a]
 gi|226899210|gb|EEH85469.1| RNA polymerase sigma factor RpoD [Escherichia sp. 3_2_53FAA]
 gi|227835188|gb|EEJ45654.1| RNA polymerase sigma factor RpoD [Escherichia coli 83972]
 gi|281180121|dbj|BAI56451.1| RNA polymerase sigma factor RpoD [Escherichia coli SE15]
 gi|294493374|gb|ADE92130.1| RNA polymerase sigma factor RpoD [Escherichia coli IHE3034]
 gi|300300014|gb|EFJ56399.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 185-1]
 gi|300410811|gb|EFJ94349.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 45-1]
 gi|305850144|gb|EFM50603.1| RNA polymerase sigma factor RpoD [Escherichia coli NC101]
 gi|307555174|gb|ADN47949.1| hypothetical protein ECABU_c34860 [Escherichia coli ABU 83972]
 gi|307625318|gb|ADN69622.1| RNA polymerase sigma factor RpoD [Escherichia coli UM146]
 gi|312947638|gb|ADR28465.1| RNA polymerase sigma factor RpoD [Escherichia coli O83:H1 str. NRG
            857C]
 gi|315288818|gb|EFU48216.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 110-3]
 gi|315295035|gb|EFU54372.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 153-1]
 gi|315297744|gb|EFU57021.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 16-3]
 gi|320195230|gb|EFW69859.1| RNA polymerase sigma factor RpoD [Escherichia coli WV_060327]
 gi|323951399|gb|EGB47274.1| RNA polymerase sigma proteinRpoD [Escherichia coli H252]
 gi|323957772|gb|EGB53486.1| RNA polymerase sigma proteinRpoD [Escherichia coli H263]
 gi|324008872|gb|EGB78091.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 57-2]
 gi|330909133|gb|EGH37647.1| RNA polymerase sigma factor RpoD [Escherichia coli AA86]
 gi|331042616|gb|EGI14758.1| RNA polymerase sigma factor RpoD [Escherichia coli M605]
 gi|331053940|gb|EGI25969.1| RNA polymerase sigma factor RpoD (Sigma-70) [Escherichia coli TA206]
 gi|333971195|gb|AEG38000.1| RNA polymerase sigma factor [Escherichia coli NA114]
 gi|355350245|gb|EHF99445.1| RNA polymerase sigma factor RpoD [Escherichia coli cloneA_i1]
 gi|355421853|gb|AER86050.1| hypothetical protein i02_3514 [Escherichia coli str. 'clone D i2']
 gi|355426773|gb|AER90969.1| hypothetical protein i14_3514 [Escherichia coli str. 'clone D i14']
 gi|371605200|gb|EHN93819.1| RNA polymerase sigma factor rpoD [Escherichia coli H397]
 gi|380346763|gb|EIA35053.1| RNA polymerase sigma factor RpoD [Escherichia coli SCI-07]
 gi|386251114|gb|EII97281.1| RNA polymerase sigma factor RpoD [Escherichia coli TW07793]
 gi|388389479|gb|EIL51008.1| RNA polymerase sigma factor RpoD [Escherichia coli KD1]
 gi|388413439|gb|EIL73431.1| RNA polymerase sigma factor RpoD [Escherichia coli HM605]
 gi|408211418|gb|EKI35964.1| RNA polymerase sigma factor [Escherichia coli 07798]
 gi|430874577|gb|ELB98133.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE4]
 gi|430884097|gb|ELC07068.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE5]
 gi|430904312|gb|ELC26021.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE16]
 gi|430905871|gb|ELC27479.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE15]
 gi|430913639|gb|ELC34760.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE25]
 gi|430928161|gb|ELC48712.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE28]
 gi|430933835|gb|ELC54226.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE39]
 gi|430942803|gb|ELC62934.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE178]
 gi|430951484|gb|ELC70704.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE187]
 gi|430961122|gb|ELC79169.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE188]
 gi|430964778|gb|ELC82224.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE189]
 gi|430971665|gb|ELC88674.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE191]
 gi|430980422|gb|ELC97182.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE201]
 gi|430991880|gb|ELD08279.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE205]
 gi|431021765|gb|ELD35086.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE214]
 gi|431026560|gb|ELD39631.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE216]
 gi|431036103|gb|ELD47479.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE220]
 gi|431049067|gb|ELD59031.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE230]
 gi|431082500|gb|ELD88814.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE47]
 gi|431089064|gb|ELD94888.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE49]
 gi|431098206|gb|ELE03529.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE53]
 gi|431105868|gb|ELE10202.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE55]
 gi|431118827|gb|ELE21846.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE58]
 gi|431122007|gb|ELE24876.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE57]
 gi|431126685|gb|ELE29032.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE60]
 gi|431129207|gb|ELE31383.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE62]
 gi|431136223|gb|ELE38092.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE67]
 gi|431147275|gb|ELE48698.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE72]
 gi|431179107|gb|ELE79014.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE86]
 gi|431188409|gb|ELE87851.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE87]
 gi|431188780|gb|ELE88221.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE93]
 gi|431232028|gb|ELF27704.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE162]
 gi|431255858|gb|ELF48936.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE6]
 gi|431263487|gb|ELF55473.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE17]
 gi|431271730|gb|ELF62849.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE18]
 gi|431272749|gb|ELF63848.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE45]
 gi|431281981|gb|ELF72879.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE23]
 gi|431300294|gb|ELF89847.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE22]
 gi|431306234|gb|ELF94547.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE46]
 gi|431325342|gb|ELG12730.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE59]
 gi|431328212|gb|ELG15532.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE63]
 gi|431336092|gb|ELG23221.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE65]
 gi|431347352|gb|ELG34245.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE84]
 gi|431366316|gb|ELG52814.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE118]
 gi|431378507|gb|ELG63498.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE123]
 gi|431393641|gb|ELG77205.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE141]
 gi|431424084|gb|ELH06181.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE192]
 gi|431429178|gb|ELH11108.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE194]
 gi|431431580|gb|ELH13355.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE165]
 gi|431437124|gb|ELH18637.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE173]
 gi|431442023|gb|ELH23130.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE175]
 gi|431461379|gb|ELH41647.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE183]
 gi|431479787|gb|ELH59520.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE207]
 gi|431487356|gb|ELH67001.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE209]
 gi|431489779|gb|ELH69404.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE211]
 gi|431492456|gb|ELH72057.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE217]
 gi|431496191|gb|ELH75775.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE215]
 gi|431503645|gb|ELH82380.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE218]
 gi|431505763|gb|ELH84368.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE223]
 gi|431511362|gb|ELH89494.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE227]
 gi|431522318|gb|ELH99553.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE229]
 gi|431528358|gb|ELI05066.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE104]
 gi|431532739|gb|ELI09289.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE106]
 gi|431541680|gb|ELI17119.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE109]
 gi|431549889|gb|ELI23964.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE113]
 gi|431567414|gb|ELI40414.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE124]
 gi|431584731|gb|ELI56706.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE129]
 gi|431599495|gb|ELI69201.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE133]
 gi|431602646|gb|ELI72076.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE137]
 gi|431613477|gb|ELI82673.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE139]
 gi|431617465|gb|ELI86481.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE145]
 gi|431624934|gb|ELI93528.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE148]
 gi|431626189|gb|ELI94741.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE150]
 gi|431632164|gb|ELJ00467.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE153]
 gi|431642204|gb|ELJ09928.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE160]
 gi|431657703|gb|ELJ24666.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE167]
 gi|431668428|gb|ELJ34954.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE174]
 gi|431671373|gb|ELJ37654.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE176]
 gi|431684839|gb|ELJ50444.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE179]
 gi|431686329|gb|ELJ51895.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE180]
 gi|431703408|gb|ELJ68095.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE85]
 gi|431703753|gb|ELJ68439.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE88]
 gi|431719020|gb|ELJ83089.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE94]
 gi|431728972|gb|ELJ92616.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE97]
 gi|431733021|gb|ELJ96463.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE99]
 gi|432346096|gb|ELL40586.1| RNA polymerase sigma factor RpoD [Escherichia coli J96]
 gi|441713761|emb|CCQ06088.1| RNA polymerase sigma factor RpoD [Escherichia coli Nissle 1917]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|157162543|ref|YP_001459861.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|170018681|ref|YP_001723635.1| RNA polymerase sigma factor RpoD [Escherichia coli ATCC 8739]
 gi|194439798|ref|ZP_03071864.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|251786344|ref|YP_003000648.1| RNA polymerase, sigma 70 (sigma D) factor, subunit of RNA polymerase
            sigma 70 [Escherichia coli BL21(DE3)]
 gi|253772097|ref|YP_003034928.1| RNA polymerase sigma factor RpoD [Escherichia coli
            'BL21-Gold(DE3)pLysS AG']
 gi|254163014|ref|YP_003046122.1| RNA polymerase sigma factor RpoD [Escherichia coli B str. REL606]
 gi|254289764|ref|YP_003055512.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|300905790|ref|ZP_07123524.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300931954|ref|ZP_07147251.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300950721|ref|ZP_07164609.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300958456|ref|ZP_07170595.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|301021226|ref|ZP_07185258.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|301301890|ref|ZP_07208024.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301644765|ref|ZP_07244740.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|312972668|ref|ZP_07786841.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|331643766|ref|ZP_08344897.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|386282180|ref|ZP_10059833.1| RNA polymerase sigma factor rpoD [Escherichia sp. 4_1_40B]
 gi|386615853|ref|YP_006135519.1| RNA polymerase sigma factor protein RpoD [Escherichia coli UMNK88]
 gi|386706317|ref|YP_006170164.1| RNA polymerase sigma factor RpoD [Escherichia coli P12b]
 gi|387613762|ref|YP_006116878.1| RNA polymerase sigma-70 factor [Escherichia coli ETEC H10407]
 gi|404376463|ref|ZP_10981623.1| RNA polymerase sigma factor rpoD [Escherichia sp. 1_1_43]
 gi|415776223|ref|ZP_11487807.1| RNA polymerase sigma factor rpoD [Escherichia coli 3431]
 gi|415861681|ref|ZP_11535291.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 85-1]
 gi|417260127|ref|ZP_12047642.1| RNA polymerase sigma factor RpoD [Escherichia coli 2.3916]
 gi|417271633|ref|ZP_12058982.1| RNA polymerase sigma factor RpoD [Escherichia coli 2.4168]
 gi|417279869|ref|ZP_12067173.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.2303]
 gi|417290957|ref|ZP_12078238.1| RNA polymerase sigma factor RpoD [Escherichia coli B41]
 gi|417614667|ref|ZP_12265122.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_EH250]
 gi|417619661|ref|ZP_12270069.1| RNA polymerase sigma factor rpoD [Escherichia coli G58-1]
 gi|417636144|ref|ZP_12286354.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_S1191]
 gi|417640959|ref|ZP_12291095.1| RNA polymerase sigma factor rpoD [Escherichia coli TX1999]
 gi|418304684|ref|ZP_12916478.1| RNA polymerase sigma factor rpoD [Escherichia coli UMNF18]
 gi|419144139|ref|ZP_13688871.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6A]
 gi|419150121|ref|ZP_13694770.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC6B]
 gi|419155532|ref|ZP_13700089.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6C]
 gi|419160883|ref|ZP_13705382.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6D]
 gi|419165933|ref|ZP_13710387.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC6E]
 gi|419171898|ref|ZP_13715779.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC7A]
 gi|419182458|ref|ZP_13726069.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7C]
 gi|419188081|ref|ZP_13731588.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7D]
 gi|419193205|ref|ZP_13736653.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC7E]
 gi|419812042|ref|ZP_14336912.1| RNA polymerase sigma factor RpoD [Escherichia coli O32:H37 str. P4]
 gi|420387310|ref|ZP_14886652.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa12]
 gi|421774970|ref|ZP_16211581.1| RNA polymerase sigma factor RpoD [Escherichia coli AD30]
 gi|422767435|ref|ZP_16821161.1| RNA polymerase sigma protein RpoD [Escherichia coli E1520]
 gi|422771058|ref|ZP_16824748.1| RNA polymerase sigma proteinRpoD [Escherichia coli E482]
 gi|422787384|ref|ZP_16840122.1| RNA polymerase sigma proteinRpoD [Escherichia coli H489]
 gi|422791634|ref|ZP_16844336.1| RNA polymerase sigma proteinRpoD [Escherichia coli TA007]
 gi|422818193|ref|ZP_16866406.1| RNA polymerase sigma factor rpoD [Escherichia coli M919]
 gi|425116608|ref|ZP_18518398.1| RNA polymerase sigma factor [Escherichia coli 8.0566]
 gi|425121364|ref|ZP_18523050.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.0569]
 gi|425274250|ref|ZP_18665650.1| RNA polymerase sigma factor [Escherichia coli TW15901]
 gi|425284833|ref|ZP_18675864.1| RNA polymerase sigma factor [Escherichia coli TW00353]
 gi|425290196|ref|ZP_18681024.1| RNA polymerase sigma factor [Escherichia coli 3006]
 gi|425306853|ref|ZP_18696535.1| RNA polymerase sigma factor [Escherichia coli N1]
 gi|427806264|ref|ZP_18973331.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
            high temperatures [Escherichia coli chi7122]
 gi|427810857|ref|ZP_18977922.1| RNA polymerase, sigma(70) factor [Escherichia coli]
 gi|432355073|ref|ZP_19598342.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE2]
 gi|432366527|ref|ZP_19609645.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE10]
 gi|432418594|ref|ZP_19661190.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE44]
 gi|432486837|ref|ZP_19728747.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE212]
 gi|432539422|ref|ZP_19776318.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE235]
 gi|432565435|ref|ZP_19802000.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE51]
 gi|432577304|ref|ZP_19813755.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE56]
 gi|432623397|ref|ZP_19859417.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE76]
 gi|432628705|ref|ZP_19864677.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE77]
 gi|432638277|ref|ZP_19874144.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE81]
 gi|432662280|ref|ZP_19897918.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE111]
 gi|432667629|ref|ZP_19903204.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE116]
 gi|432672160|ref|ZP_19907685.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE119]
 gi|432686891|ref|ZP_19922184.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE156]
 gi|432688258|ref|ZP_19923533.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE161]
 gi|432705814|ref|ZP_19940910.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE171]
 gi|432738556|ref|ZP_19973310.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE42]
 gi|432876995|ref|ZP_20094864.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE154]
 gi|432956813|ref|ZP_20148433.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE197]
 gi|433054707|ref|ZP_20241874.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE122]
 gi|433121638|ref|ZP_20307301.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE157]
 gi|433131630|ref|ZP_20317060.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE163]
 gi|433136283|ref|ZP_20321620.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE166]
 gi|433174959|ref|ZP_20359474.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE232]
 gi|442597135|ref|ZP_21014931.1| RNA polymerase sigma factor RpoD [Escherichia coli O5:K4(L):H4 str.
            ATCC 23502]
 gi|443619134|ref|YP_007382990.1| RNA polymerase sigma-70 factor [Escherichia coli APEC O78]
 gi|157068223|gb|ABV07478.1| RNA polymerase sigma factor RpoD [Escherichia coli HS]
 gi|169753609|gb|ACA76308.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli ATCC 8739]
 gi|194421246|gb|EDX37267.1| RNA polymerase sigma factor RpoD [Escherichia coli 101-1]
 gi|226839861|gb|EEH71882.1| RNA polymerase sigma factor rpoD [Escherichia sp. 1_1_43]
 gi|242378617|emb|CAQ33404.1| RNA polymerase, sigma 70 (sigma D) factor, subunit of RNA polymerase
            sigma 70 [Escherichia coli BL21(DE3)]
 gi|253323141|gb|ACT27743.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli
            'BL21-Gold(DE3)pLysS AG']
 gi|253974915|gb|ACT40586.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979071|gb|ACT44741.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|299881584|gb|EFI89795.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 196-1]
 gi|300314897|gb|EFJ64681.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 175-1]
 gi|300402389|gb|EFJ85927.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 84-1]
 gi|300449958|gb|EFK13578.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 116-1]
 gi|300460377|gb|EFK23870.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 187-1]
 gi|300842871|gb|EFK70631.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 124-1]
 gi|301076919|gb|EFK91725.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 146-1]
 gi|309703498|emb|CBJ02838.1| RNA polymerase sigma-70 factor [Escherichia coli ETEC H10407]
 gi|310332610|gb|EFP99823.1| RNA polymerase sigma factor rpoD [Escherichia coli 1827-70]
 gi|315256981|gb|EFU36949.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 85-1]
 gi|315617141|gb|EFU97750.1| RNA polymerase sigma factor rpoD [Escherichia coli 3431]
 gi|323935931|gb|EGB32226.1| RNA polymerase sigma protein RpoD [Escherichia coli E1520]
 gi|323941835|gb|EGB38014.1| RNA polymerase sigma proteinRpoD [Escherichia coli E482]
 gi|323960998|gb|EGB56615.1| RNA polymerase sigma proteinRpoD [Escherichia coli H489]
 gi|323971810|gb|EGB67035.1| RNA polymerase sigma proteinRpoD [Escherichia coli TA007]
 gi|331037237|gb|EGI09461.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 gi|332345022|gb|AEE58356.1| RNA polymerase sigma factor protein RpoD [Escherichia coli UMNK88]
 gi|339416782|gb|AEJ58454.1| RNA polymerase sigma factor rpoD [Escherichia coli UMNF18]
 gi|345360513|gb|EGW92682.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_EH250]
 gi|345372791|gb|EGX04754.1| RNA polymerase sigma factor rpoD [Escherichia coli G58-1]
 gi|345385862|gb|EGX15699.1| RNA polymerase sigma factor rpoD [Escherichia coli STEC_S1191]
 gi|345392255|gb|EGX22039.1| RNA polymerase sigma factor rpoD [Escherichia coli TX1999]
 gi|377990379|gb|EHV53540.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC6B]
 gi|377991670|gb|EHV54820.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6A]
 gi|377994494|gb|EHV57620.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6C]
 gi|378005739|gb|EHV68739.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC6D]
 gi|378008862|gb|EHV71821.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC6E]
 gi|378013685|gb|EHV76602.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC7A]
 gi|378022578|gb|EHV85265.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7C]
 gi|378025830|gb|EHV88470.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC7D]
 gi|378036602|gb|EHV99142.1| RNA polymerase sigma factor rpoD [Escherichia coli DEC7E]
 gi|383104485|gb|AFG41994.1| RNA polymerase sigma factor RpoD [Escherichia coli P12b]
 gi|385155017|gb|EIF17023.1| RNA polymerase sigma factor RpoD [Escherichia coli O32:H37 str. P4]
 gi|385538706|gb|EIF85568.1| RNA polymerase sigma factor rpoD [Escherichia coli M919]
 gi|386120556|gb|EIG69180.1| RNA polymerase sigma factor rpoD [Escherichia sp. 4_1_40B]
 gi|386226175|gb|EII48485.1| RNA polymerase sigma factor RpoD [Escherichia coli 2.3916]
 gi|386235333|gb|EII67309.1| RNA polymerase sigma factor RpoD [Escherichia coli 2.4168]
 gi|386237199|gb|EII74145.1| RNA polymerase sigma factor RpoD [Escherichia coli 3.2303]
 gi|386253279|gb|EIJ02969.1| RNA polymerase sigma factor RpoD [Escherichia coli B41]
 gi|391303595|gb|EIQ61431.1| RNA polymerase sigma factor rpoD [Escherichia coli EPECa12]
 gi|408191323|gb|EKI16936.1| RNA polymerase sigma factor [Escherichia coli TW15901]
 gi|408200286|gb|EKI25469.1| RNA polymerase sigma factor [Escherichia coli TW00353]
 gi|408211691|gb|EKI36236.1| RNA polymerase sigma factor [Escherichia coli 3006]
 gi|408226711|gb|EKI50344.1| RNA polymerase sigma factor [Escherichia coli N1]
 gi|408460047|gb|EKJ83827.1| RNA polymerase sigma factor RpoD [Escherichia coli AD30]
 gi|408565507|gb|EKK41591.1| RNA polymerase sigma factor [Escherichia coli 8.0566]
 gi|408566507|gb|EKK42574.1| RNA polymerase sigma factor rpoD [Escherichia coli 8.0569]
 gi|412964446|emb|CCK48374.1| RNA polymerase, sigma(70) factor; regulation of proteins induced at
            high temperatures [Escherichia coli chi7122]
 gi|412971036|emb|CCJ45688.1| RNA polymerase, sigma(70) factor [Escherichia coli]
 gi|430873981|gb|ELB97547.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE2]
 gi|430891866|gb|ELC14387.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE10]
 gi|430937872|gb|ELC58126.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE44]
 gi|431014524|gb|ELD28232.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE212]
 gi|431067835|gb|ELD76351.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE235]
 gi|431091294|gb|ELD97039.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE51]
 gi|431113470|gb|ELE17134.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE56]
 gi|431157479|gb|ELE58121.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE76]
 gi|431161998|gb|ELE62467.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE77]
 gi|431169692|gb|ELE69911.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE81]
 gi|431198354|gb|ELE97179.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE111]
 gi|431199021|gb|ELE97802.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE116]
 gi|431209007|gb|ELF07128.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE119]
 gi|431220865|gb|ELF18198.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE156]
 gi|431236887|gb|ELF32084.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE161]
 gi|431241598|gb|ELF36034.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE171]
 gi|431280611|gb|ELF71527.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE42]
 gi|431418959|gb|ELH01353.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE154]
 gi|431465797|gb|ELH45878.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE197]
 gi|431567587|gb|ELI40580.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE122]
 gi|431640409|gb|ELJ08169.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE157]
 gi|431644367|gb|ELJ12029.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE163]
 gi|431654942|gb|ELJ21989.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE166]
 gi|431690246|gb|ELJ55730.1| RNA polymerase sigma factor rpoD [Escherichia coli KTE232]
 gi|441654295|emb|CCQ00844.1| RNA polymerase sigma factor RpoD [Escherichia coli O5:K4(L):H4 str.
            ATCC 23502]
 gi|443423642|gb|AGC88546.1| RNA polymerase sigma-70 factor [Escherichia coli APEC O78]
          Length = 613

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|107099562|ref|ZP_01363480.1| hypothetical protein PaerPA_01000575 [Pseudomonas aeruginosa PACS2]
          Length = 604

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 313/603 (51%), Positives = 418/603 (69%), Gaps = 10/603 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            +I  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L+   
Sbjct: 1    MIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLLAEAD 60

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
            +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 61   TDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 120

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE---- 1009
             AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++     
Sbjct: 121  SAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDSADSK 180

Query: 1010 ----EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
                E+   + SS             E+ ++F+ +S   DK +KA +K G  S+      
Sbjct: 181  EKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQATAEL 240

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++FP +
Sbjct: 241  TGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNH 300

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M  GE
Sbjct: 301  ETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 360

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 361  AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 420

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+M
Sbjct: 421  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDM 480

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +++L 
Sbjct: 481  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 540

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ 
Sbjct: 541  GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHLRS 600

Query: 1426 FLE 1428
            FL+
Sbjct: 601  FLD 603



 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 306/590 (51%), Positives = 409/590 (69%), Gaps = 10/590 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           +I  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L+   
Sbjct: 1   MIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLLAEAD 60

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
           +D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++
Sbjct: 61  TDEAAAEEAAAALAAVESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVM 120

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE---- 219
            AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++     
Sbjct: 121 SAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDSADSK 180

Query: 220 ----EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
               E+   + SS             E+ ++F+ +S   DK +KA +K G  S+      
Sbjct: 181 EKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQATAEL 240

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++FP +
Sbjct: 241 TGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRLFPNH 300

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M  GE
Sbjct: 301 ETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGE 360

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 361 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 420

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+M
Sbjct: 421 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDM 480

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +++L 
Sbjct: 481 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTREVLA 540

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 590


>gi|123443868|ref|YP_001007839.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            enterocolitica 8081]
 gi|420260054|ref|ZP_14762743.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            enterocolitica WA-314]
 gi|122090829|emb|CAL13711.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            enterocolitica 8081]
 gi|404512463|gb|EKA26309.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
            enterocolitica WA-314]
          Length = 612

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 310/617 (50%), Positives = 417/617 (67%), Gaps = 23/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182  HVGSELSTEEMDDDDDEDEDDEEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239  ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295  KMPKKNFVTLFTSNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 595  RKLRHPSRSEVLRSFLD 611



 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/604 (50%), Positives = 408/604 (67%), Gaps = 23/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182 HVGSELSTEEMDDDDDEDEDDEEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239 ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295 KMPKKNFVTLFTSNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 622 RKLR 625
           RKLR
Sbjct: 595 RKLR 598


>gi|359439239|ref|ZP_09229216.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20311]
 gi|359445897|ref|ZP_09235611.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20439]
 gi|358026066|dbj|GAA65465.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20311]
 gi|358040300|dbj|GAA71860.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20439]
          Length = 614

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 317/607 (52%), Positives = 416/607 (68%), Gaps = 8/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN-EE 1010
              +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +   E
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDADEAPPIAATNIGSELSE 187

Query: 1011 KILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            K L +S   D  ++  ++ +        E+ I F N+   + K R+ F+K+G +      
Sbjct: 188  KQLDDSDDDDDDSDDEDEEEVDTGPDPEEARIHFENLRDLYTKARETFDKKGRSHPESQA 247

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F 
Sbjct: 248  AILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFA 307

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  
Sbjct: 308  NNETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSI 367

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M
Sbjct: 428  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERM 487

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+
Sbjct: 488  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDV 547

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 548  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 607

Query: 1424 KIFLEGK 1430
            K FL+ K
Sbjct: 608  KSFLDAK 614



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 311/600 (51%), Positives = 409/600 (68%), Gaps = 9/600 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN-EE 220
             +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +   E
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDADEAPPIAATNIGSELSE 187

Query: 221 KILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           K L +S   D  ++  ++ +        E+ I F N+   + K R+ F+K+G +      
Sbjct: 188 KQLDDSDDDDDDSDDEDEEEVDTGPDPEEARIHFENLRDLYTKARETFDKKGRSHPESQA 247

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F 
Sbjct: 248 AILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFA 307

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  
Sbjct: 308 NNETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSI 367

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERM 487

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+
Sbjct: 488 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDV 547

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 607


>gi|59712861|ref|YP_205637.1| RNA polymerase sigma factor RpoD [Vibrio fischeri ES114]
 gi|59480962|gb|AAW86749.1| RNA polymerase, sigma-70 (sigma-D) factor [Vibrio fischeri ES114]
          Length = 613

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 310/624 (49%), Positives = 426/624 (68%), Gaps = 36/624 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63   DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 1000
            I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N   ++  
Sbjct: 119  IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKE 1054
               +  +   +  ++    + +  + E+ +        +L KF+ +   +  M+ AFE+ 
Sbjct: 179  TATHIGSELSESELDDEDDEDAEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239  GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 1164
            +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299  KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349  KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469  QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
              P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529  ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  QIEAKALRKLRHPSRSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/611 (49%), Positives = 417/611 (68%), Gaps = 36/611 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63  DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV 210
           I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N   ++  
Sbjct: 119 IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKE 264
              +  +   +  ++    + +  + E+ +        +L KF+ +   +  M+ AFE+ 
Sbjct: 179 TATHIGSELSESELDDEDDEDAEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239 GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 374
           +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299 KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349 KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469 QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
             P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529 ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 589 QIEAKALRKLR 599


>gi|423686991|ref|ZP_17661799.1| RNA polymerase sigma factor RpoD [Vibrio fischeri SR5]
 gi|371493750|gb|EHN69350.1| RNA polymerase sigma factor RpoD [Vibrio fischeri SR5]
          Length = 613

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 315/624 (50%), Positives = 427/624 (68%), Gaps = 36/624 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63   DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSN 997
            I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N    S+ 
Sbjct: 119  IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKE 1054
                 G++ +  E    +    +  TE+ E    +   +L KF+ +   +  M+ AFE+ 
Sbjct: 179  TATHIGSELSEAELDDEDDEDEEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239  GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 1164
            +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299  KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349  KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469  QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
              P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529  ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  QIEAKALRKLRHPSRSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/611 (50%), Positives = 418/611 (68%), Gaps = 36/611 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63  DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSN 207
           I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N    S+ 
Sbjct: 119 IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKE 264
                G++ +  E    +    +  TE+ E    +   +L KF+ +   +  M+ AFE+ 
Sbjct: 179 TATHIGSELSEAELDDEDDEDEEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239 GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 374
           +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299 KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349 KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469 QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
             P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529 ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 589 QIEAKALRKLR 599


>gi|197335189|ref|YP_002157048.1| RNA polymerase sigma factor RpoD [Vibrio fischeri MJ11]
 gi|197316679|gb|ACH66126.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
          Length = 613

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 315/624 (50%), Positives = 427/624 (68%), Gaps = 36/624 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 940
            + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63   DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSN 997
            I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N    S+ 
Sbjct: 119  IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKE 1054
                 G++ +  E    +    +  TE+ E    +   +L KF+ +   +  M+ AFE+ 
Sbjct: 179  TATHIGSELSEAELDDEDDEDDEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239  GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 1164
            +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299  KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349  KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469  QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
              P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529  ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   L+ FL+
Sbjct: 589  QIEAKALRKLRHPSRSEVLRSFLD 612



 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/611 (50%), Positives = 418/611 (68%), Gaps = 36/611 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSDDDV------EEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGE 150
           + + L+    DDD        EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GE
Sbjct: 63  DDMSLN----DDDAVTDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGE 118

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSN 207
           I+IAKRIEEG+ ++  +++  P  I  +L   DK+   EI++ +I+ G +D N    S+ 
Sbjct: 119 IDIAKRIEEGINEVQCSVAEFPGAISYLLEQFDKVQTEEIRLTDIISGFVDPNDDGSSAP 178

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE---SLIKFSNISFHFDKMRKAFEKE 264
                G++ +  E    +    +  TE+ E    +   +L KF+ +   +  M+ AFE+ 
Sbjct: 179 TATHIGSELSEAELDDEDDEDDEGETEEEEDAGIDPELALEKFTELRTSYHNMQLAFEEF 238

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +     +A   +++     +   K  + L   +R+ +++V   E+ I+ + V    MP
Sbjct: 239 GRDDAKSREAIGELTDIFREFKLIPKQFDYLVKEMRDGMDRVRTQERLIMRMCVEYGKMP 298

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQ 374
           +  FI +F  NE +  W          +N I+  + P ++ LQ+          KL +++
Sbjct: 299 KKSFIALFTGNESSDEW----------FNEIMASDKPYVERLQRYEEDIRRSIAKLDSIE 348

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  LP+ +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 349 KETGLPVENIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 468

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 469 QMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTL 528

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
             P D+A + S++    D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 529 ELPVDSATSTSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 589 QIEAKALRKLR 599


>gi|238789198|ref|ZP_04632986.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC 33641]
 gi|238722730|gb|EEQ14382.1| RNA polymerase sigma factor rpoD [Yersinia frederiksenii ATCC 33641]
          Length = 612

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 310/617 (50%), Positives = 417/617 (67%), Gaps = 23/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182  HVGSELSTEEMDDDDDEDEDDDEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239  ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295  KMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 595  RKLRHPSRSEVLRSFLD 611



 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/604 (50%), Positives = 408/604 (67%), Gaps = 23/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E          D   +  E+    S+       KFS +   ++  R   +K G   
Sbjct: 182 HVGSELSTEEMDDDDDEDEDDDEEEDDNSIDPELARQKFSELREQYENARLEIKKNG--- 238

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
               ++H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 239 ----RSHANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 294

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W      +   ++  L      ++   QKL  ++ +  L +
Sbjct: 295 KMPKKNFVTLFASNETSDTWFAAAIAMGKPWSEKLKDVSDDVQRSLQKLRQIEEETGLTI 354

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 355 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 414

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 415 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 474

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 475 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 534

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 622 RKLR 625
           RKLR
Sbjct: 595 RKLR 598


>gi|359434727|ref|ZP_09224978.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20652]
 gi|357918636|dbj|GAA61227.1| RNA polymerase primary sigma factor [Pseudoalteromonas sp. BSi20652]
          Length = 615

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 321/621 (51%), Positives = 414/621 (66%), Gaps = 35/621 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128  NQVQISVAEYPEAITYLLDQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 1012 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 1049
            I   +  ++LS +QL+  K                       E+ I F N+   ++K R 
Sbjct: 175  ISATNIGSELSAKQLDDDKDDKDDVDSDDEDEEEVDTGPDPEEARIHFENLRDLYNKARD 234

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235  TFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRIQERLIMKQAVQ 294

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
               +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L
Sbjct: 295  IAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTGL 354

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355  SIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475  MGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535  SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHPSR   LK FL+ K
Sbjct: 595  ALRKLRHPSRSDLLKSFLDAK 615



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 315/614 (51%), Positives = 407/614 (66%), Gaps = 36/614 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +I+ G ID N              +   
Sbjct: 128 NQVQISVAEYPEAITYLLDQWDKFEAEEMRLSDIIVGFIDPN-------------EDTAP 174

Query: 222 ILIESSSADLSTEQLEKLKY----------------------ESLIKFSNISFHFDKMRK 259
           I   +  ++LS +QL+  K                       E+ I F N+   ++K R 
Sbjct: 175 ISATNIGSELSAKQLDDDKDDKDDVDSDDEDEEEVDTGPDPEEARIHFENLRDLYNKARD 234

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
            FE +G +      A   I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 235 TFEAKGRSHPESQAAIFEIGELFRTFKLIPKQFDRMVNNMREMMDRVRIQERLIMKQAVQ 294

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
              +P+  F+K F  NE + +WVD E      Y+  L    P I     KL  ++    L
Sbjct: 295 IAKLPKKTFVKHFANNETDASWVDLEISGNEKYSAKLEEVKPEIIRSINKLSVIEQTTGL 354

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 355 SIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 414

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 415 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 474

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP+P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 475 MGREPNPEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPID 534

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A   S+R    D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 535 SATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 594

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 595 ALRKLRHPSRSDLL 608


>gi|301325578|ref|ZP_07219046.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
 gi|300847629|gb|EFK75389.1| RNA polymerase sigma factor RpoD [Escherichia coli MS 78-1]
          Length = 613

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 301/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDPTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDPTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|45442721|ref|NP_994260.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
            str. 91001]
 gi|45437587|gb|AAS63137.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus
            str. 91001]
          Length = 631

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 309/617 (50%), Positives = 416/617 (67%), Gaps = 23/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 22   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 81

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 82   DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 142  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 200

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 1058
               +E          +   E  +     S+       KFS++   ++  R   +K G N 
Sbjct: 201  HVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYENARMEIKKNGRN- 259

Query: 1059 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
                  H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 260  ------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 313

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+ +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +
Sbjct: 314  KMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQKLRQIEEETGLTI 373

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 374  EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 433

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++ ISRQ+LQE G
Sbjct: 434  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNGISRQMLQEMG 493

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 494  REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 553

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 554  TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 613

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 614  RKLRHPSRSEVLRSFLD 630



 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/604 (50%), Positives = 407/604 (67%), Gaps = 23/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 22  QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVLEEAPDA 81

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + LML+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 82  DDLMLAENTTDTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N +  +      
Sbjct: 142 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLITGFVDPN-AEEDIAPTAT 200

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESL------IKFSNISFHFDKMRKAFEKEGYNS 268
              +E          +   E  +     S+       KFS++   ++  R   +K G N 
Sbjct: 201 HVGSELSTEEMDDEDEDEDEDDDAEDDNSIDPELARQKFSDLREQYENARMEIKKNGRN- 259

Query: 269 ESYIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
                 H N + E+L +       R   K  + L + +R  +++V   E+ I+++ V +C
Sbjct: 260 ------HANAAAEILKLSEVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERIIMKLCVEQC 313

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+ +F+ +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +
Sbjct: 314 KMPKKNFVTLFSSNETSDTWFNAAVAMGKPWSEKLKDVSEDVQRSLQKLRQIEEETGLTI 373

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 374 EQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 433

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++ ISRQ+LQE G
Sbjct: 434 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNGISRQMLQEMG 493

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 494 REPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 553

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 554 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 613

Query: 622 RKLR 625
           RKLR
Sbjct: 614 RKLR 617


>gi|418584852|ref|ZP_13148909.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa MPAO1/P1]
 gi|375045184|gb|EHS37770.1| RNA polymerase sigma factor RpoD [Pseudomonas aeruginosa MPAO1/P1]
          Length = 617

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 314/607 (51%), Positives = 419/607 (69%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10   RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+   E   AAL+  +SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70   AEADTDEAAAEEAAAALAAXESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 1009
            ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130  REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 1010 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                    E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190  ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
                  ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250  TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310  FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490  RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 610  HLRSFLD 616



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 307/594 (51%), Positives = 410/594 (69%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT++E+ND LPEDI D E +E II+    M I+V E   D + L+L
Sbjct: 10  RLKELIARGREQGYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGINVFETAPDADALLL 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+   E   AAL+  +SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+
Sbjct: 70  AEADTDEAAAEEAAAALAAXESDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGI 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS--NNRVIKGNKNNNE 219
           ++++ AI+  P T+  IL   ++I     ++ +++ G ID +  S     V   N  ++ 
Sbjct: 130 REVMSAIAQFPGTVDSILADYNRIVAEGGRLSDVLSGYIDPDDGSLPAEEVEPVNLKDDS 189

Query: 220 --------EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                   E+   + SS             E+ ++F+ +S   DK +KA +K G  S+  
Sbjct: 190 ADSKEKDDEEEESDDSSDSDDEGDGGPDPEEARLRFTAVSEQLDKAKKALKKHGRGSKQA 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
                 ++   + I+   K  + L   +R+ +  V   E+ I+++ V    MPR  F+++
Sbjct: 250 TAELTGLAELFMPIKLVPKQFDALVARVRSALEGVRAQERAIMQLCVRDARMPRADFLRL 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           FP +E +  WVD+  K +  Y   + R    I   QQKL  L++++ L + ++++INR M
Sbjct: 310 FPNHETDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P + A + S++   +
Sbjct: 490 RMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIEMATSESLKESTR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|392556746|ref|ZP_10303883.1| RNA polymerase sigma factor [Pseudoalteromonas undina NCIMB 2128]
          Length = 613

 Score =  578 bits (1489), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 316/606 (52%), Positives = 415/606 (68%), Gaps = 7/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN--NE 1009
              +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +  +E
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDADEAPPIAATNIGSELSE 187

Query: 1010 EKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            +++       D   E  E++       E+ I F N+   + K R+ F+K+G +      A
Sbjct: 188  KQLDDSDDDDDSDDEDEEEVDTGPDPEEARIHFENLRDLYTKARETFDKKGRSHPESQAA 247

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
               I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F  
Sbjct: 248  ILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFAN 307

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  G
Sbjct: 308  NETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLSSMEESTGLSIERIKDINRRMSIG 367

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 368  EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M 
Sbjct: 428  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMM 487

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+L
Sbjct: 488  MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVL 547

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK
Sbjct: 548  AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLLK 607

Query: 1425 IFLEGK 1430
             FL+ K
Sbjct: 608  SFLDAK 613



 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 310/599 (51%), Positives = 408/599 (68%), Gaps = 8/599 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN--NE 219
             +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +  +E
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDADEAPPIAATNIGSELSE 187

Query: 220 EKILIESSSADLSTEQLEKLKY-----ESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           +++       D   E  E++       E+ I F N+   + K R+ F+K+G +      A
Sbjct: 188 KQLDDSDDDDDSDDEDEEEVDTGPDPEEARIHFENLRDLYTKARETFDKKGRSHPESQAA 247

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
              I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F  
Sbjct: 248 ILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFAN 307

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  G
Sbjct: 308 NETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLSSMEESTGLSIERIKDINRRMSIG 367

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 368 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M 
Sbjct: 428 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERMM 487

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+L
Sbjct: 488 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDVL 547

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 548 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 606


>gi|339050950|ref|ZP_08647764.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
 gi|330721841|gb|EGG99811.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
          Length = 614

 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/611 (51%), Positives = 416/611 (68%), Gaps = 12/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  R + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    M I+V E   D 
Sbjct: 6    EQQRSRLKELIARGKEQGYLTYAEVNDHLPQDISDPDQVEDIIRMINDMGITVDEVAPDQ 65

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            +TL L N  +DDD  E   AAL+ V+++ GRT DP++MYMREMGSVELLTR+GEI IAKR
Sbjct: 66   DTLQL-NENTDDDAVEEAAAALAAVETEVGRTTDPVRMYMREMGSVELLTREGEIVIAKR 124

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEG+++++ A++S P  +  IL A  +  + E +I +I+ G ++        VI+G + 
Sbjct: 125  IEEGIREVMCALASFPGAVDVILEAYAQTIEEEGRISDILSGFLEDEVEEP--VIQGQQA 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLK---------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +    +     + +  ++ +          E+  + S +   F+ + KA EK G  
Sbjct: 183  PQPVEETDVTVDETDTDDSDDEDEDEVERGPDPVETAERMSALKKQFEIVNKAIEKHGRG 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+  ++A   +      I+ T +  ++L   +R  +  +   E+ IL        MPR  
Sbjct: 243  SKQVLEAQEELGEIFCPIKLTPRYFDRLVQNVRETLEFIRAQERLILHTCTRTVRMPRKA 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FIK F  +E +  W+D   +  HDY+  L  +   I   Q+KL   +  I  P++++++I
Sbjct: 303  FIKEFMGSETDPAWLDRAIEGGHDYSEGLAEHREDIVRAQRKLKTTEESIDAPIHEIKEI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRHMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D+A    + 
Sbjct: 483  ELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNIDSPIDSATAEGLS 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               + +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  EATRGVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSDHLRGFLD 613



 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 305/598 (51%), Positives = 407/598 (68%), Gaps = 12/598 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  R + K LI  GKE+GYLT++E+ND LP+DI D + +E II+    M I+V E   D 
Sbjct: 6   EQQRSRLKELIARGKEQGYLTYAEVNDHLPQDISDPDQVEDIIRMINDMGITVDEVAPDQ 65

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           +TL L N  +DDD  E   AAL+ V+++ GRT DP++MYMREMGSVELLTR+GEI IAKR
Sbjct: 66  DTLQL-NENTDDDAVEEAAAALAAVETEVGRTTDPVRMYMREMGSVELLTREGEIVIAKR 124

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEG+++++ A++S P  +  IL A  +  + E +I +I+ G ++        VI+G + 
Sbjct: 125 IEEGIREVMCALASFPGAVDVILEAYAQTIEEEGRISDILSGFLEDEVEEP--VIQGQQA 182

Query: 217 NNEEKILIESSSADLSTEQLEKLK---------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +    +     + +  ++ +          E+  + S +   F+ + KA EK G  
Sbjct: 183 PQPVEETDVTVDETDTDDSDDEDEDEVERGPDPVETAERMSALKKQFEIVNKAIEKHGRG 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S+  ++A   +      I+ T +  ++L   +R  +  +   E+ IL        MPR  
Sbjct: 243 SKQVLEAQEELGEIFCPIKLTPRYFDRLVQNVRETLEFIRAQERLILHTCTRTVRMPRKA 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FIK F  +E +  W+D   +  HDY+  L  +   I   Q+KL   +  I  P++++++I
Sbjct: 303 FIKEFMGSETDPAWLDRAIEGGHDYSEGLAEHREDIVRAQRKLKTTEESIDAPIHEIKEI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRHMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D+A    + 
Sbjct: 483 ELGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNIDSPIDSATAEGLS 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              + +L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 EATRGVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|332307721|ref|YP_004435572.1| RNA polymerase sigma-70 subunit RpoD [Glaciecola sp. 4H-3-7+YE-5]
 gi|332175050|gb|AEE24304.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. 4H-3-7+YE-5]
          Length = 613

 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/621 (49%), Positives = 422/621 (67%), Gaps = 28/621 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 2    VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 61

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62   SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 122  RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 181

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 1057
             +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 182  GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 241

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                 K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 242  HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 301

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FIK F  NE + +W+         Y L +  + P ++EL+           K+  ++ + 
Sbjct: 302  FIKAFSGNETSTDWL---------YEL-MASDAPYVEELKVHQEELERSIGKMNAVEEET 351

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 352  GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 411

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 412  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 471

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 472  QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 531

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 532  LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 591

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR  +L+ FL+
Sbjct: 592  AKALRKLRHPSRSEQLRSFLD 612



 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 412/608 (67%), Gaps = 28/608 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 2   VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 61

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62  SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 122 RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 181

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 267
            +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 182 GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 241

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
                K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 242 HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 301

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FIK F  NE + +W+         Y L +  + P ++EL+           K+  ++ + 
Sbjct: 302 FIKAFSGNETSTDWL---------YEL-MASDAPYVEELKVHQEELERSIGKMNAVEEET 351

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 352 GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 411

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 412 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 471

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 472 QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 531

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 532 LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 591

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 592 AKALRKLR 599


>gi|71282406|ref|YP_270983.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
 gi|71148146|gb|AAZ28619.1| RNA polymerase sigma-70 factor [Colwellia psychrerythraea 34H]
          Length = 616

 Score =  578 bits (1489), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/616 (50%), Positives = 418/616 (67%), Gaps = 24/616 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLTF+++ND LP+DIID + +E I+     M I V E+  D +TLM+
Sbjct: 8    RLKDLITKGKEQGYLTFAQVNDHLPQDIIDSDQVEDIVSMINDMGIQVFENAPDQDTLMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +   +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR GEI IAKRIEEG+
Sbjct: 68   AEANTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTRKGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
            K++  ++S  P  I  +L   D     E+++ +I+ G +D +   ++         +E  
Sbjct: 128  KEVQRSVSEYPPAINYLLDMWDNFEAEEVRLTDIIIGFLDPDAEDDDVAAAATHVGSE-- 185

Query: 1012 ILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFHFDKMRKAFEKE 1054
                 S  DL+ E  EK + ++                   KF+ +    +   K  +K+
Sbjct: 186  ----LSKEDLANEDSEKKEGDAEEEDEEEEDTGPDPELAREKFTLLREAHENATKVVKKK 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G   +   +A + ++      R   K  +KL   +R  ++++   E+ I++  V+  GMP
Sbjct: 242  GRGHKDAQEAIDAVAEVFKEFRLIPKLFDKLVKNMRGMMDRLRVQERLIMKHCVS-AGMP 300

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  FIK+FP NE +  W + E    + Y+  L      ++    KL  ++ +  L ++ +
Sbjct: 301  KTTFIKIFPGNETSKEWFEAEKAAGNPYSTKLGDIEHDVERCIYKLNQIEEETHLNIHGI 360

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 361  KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 420

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP
Sbjct: 421  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREP 480

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +   P D+A + 
Sbjct: 481  TPEELAERMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGSGELPVDSATSE 540

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            +++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 541  NLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 600

Query: 1415 RHPSRYYKLKIFLEGK 1430
            RHPSR  +LK FL+G+
Sbjct: 601  RHPSRSEQLKSFLDGE 616



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 302/601 (50%), Positives = 406/601 (67%), Gaps = 24/601 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLTF+++ND LP+DIID + +E I+     M I V E+  D +TLM+
Sbjct: 8   RLKDLITKGKEQGYLTFAQVNDHLPQDIIDSDQVEDIVSMINDMGIQVFENAPDQDTLMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +   +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR GEI IAKRIEEG+
Sbjct: 68  AEANTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTRKGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
           K++  ++S  P  I  +L   D     E+++ +I+ G +D +   ++         +E  
Sbjct: 128 KEVQRSVSEYPPAINYLLDMWDNFEAEEVRLTDIIIGFLDPDAEDDDVAAAATHVGSE-- 185

Query: 222 ILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFHFDKMRKAFEKE 264
                S  DL+ E  EK + ++                   KF+ +    +   K  +K+
Sbjct: 186 ----LSKEDLANEDSEKKEGDAEEEDEEEEDTGPDPELAREKFTLLREAHENATKVVKKK 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G   +   +A + ++      R   K  +KL   +R  ++++   E+ I++  V+  GMP
Sbjct: 242 GRGHKDAQEAIDAVAEVFKEFRLIPKLFDKLVKNMRGMMDRLRVQERLIMKHCVS-AGMP 300

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  FIK+FP NE +  W + E    + Y+  L      ++    KL  ++ +  L ++ +
Sbjct: 301 KTTFIKIFPGNETSKEWFEAEKAAGNPYSTKLGDIEHDVERCIYKLNQIEEETHLNIHGI 360

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 361 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 420

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP
Sbjct: 421 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREP 480

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED +   P D+A + 
Sbjct: 481 TPEELAERMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGSGELPVDSATSE 540

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           +++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 541 NLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 600

Query: 625 R 625
           R
Sbjct: 601 R 601


>gi|388259245|ref|ZP_10136419.1| transcription initiation factor sigma 70 [Cellvibrio sp. BR]
 gi|387937203|gb|EIK43760.1| transcription initiation factor sigma 70 [Cellvibrio sp. BR]
          Length = 618

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/619 (49%), Positives = 418/619 (67%), Gaps = 18/619 (2%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 883
            E+++  + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E  
Sbjct: 3    EDVQQQQSRIKELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIRVYETA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVD--SDFGRTKDPIKMYMREMGSVELLTRDGEI 941
             D +TL++++  S  D   A EAA + V   ++ GRT DP++MYMREMG+VELLTR+GEI
Sbjct: 63   PDADTLLMTDGDSAADEIAAAEAAAALVAVETETGRTTDPVRMYMREMGTVELLTREGEI 122

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------- 991
             IAKRIEEG+++++HAI+  P  + ++L     ++K E ++ +++ G +D          
Sbjct: 123  VIAKRIEEGVRELMHAIAYWPGAVQQVLDEYALVAKEERRLADVIIGWLDPVEDIPAALA 182

Query: 992  --KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
              +         K   ++ EE+   E     +S    E    E+  +F  +    DK  K
Sbjct: 183  EVEEIPVAAAGAKPAADDEEEETATEDEEEAVSGVDPE----EARARFEELQKQHDKTTK 238

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A  K GY S+   K  + + +     +  A+  E +    R  ++ V + E+ I+++   
Sbjct: 239  ALAKYGYGSKQAEKELSALGDLFKFFKLPARQFEPIYSKARVALDSVRKHERHIMDLCTR 298

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
            +  M R  FIK FP NE N  W+ +  K + +    L R +P ++  QQ+L  ++ +  L
Sbjct: 299  RAQMQRKTFIKEFPGNETNEAWLPDFLKGKVEAPEKLERVLPDVQSAQQQLAQIEAESGL 358

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             L  ++DINR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359  SLASIKDINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE
Sbjct: 419  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQE 478

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P +
Sbjct: 479  MGREPTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIISPVE 538

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A    +    +++L  LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 539  SATMEGLMEATREVLAGLTAREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAK 598

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 599  ALRKLRHPSRSDHLRSFLD 617



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/606 (49%), Positives = 409/606 (67%), Gaps = 18/606 (2%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV 93
           E+++  + + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E  
Sbjct: 3   EDVQQQQSRIKELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIRVYETA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVD--SDFGRTKDPIKMYMREMGSVELLTRDGEI 151
            D +TL++++  S  D   A EAA + V   ++ GRT DP++MYMREMG+VELLTR+GEI
Sbjct: 63  PDADTLLMTDGDSAADEIAAAEAAAALVAVETETGRTTDPVRMYMREMGTVELLTREGEI 122

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------- 201
            IAKRIEEG+++++HAI+  P  + ++L     ++K E ++ +++ G +D          
Sbjct: 123 VIAKRIEEGVRELMHAIAYWPGAVQQVLDEYALVAKEERRLADVIIGWLDPVEDIPAALA 182

Query: 202 --KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
             +         K   ++ EE+   E     +S    E    E+  +F  +    DK  K
Sbjct: 183 EVEEIPVAAAGAKPAADDEEEETATEDEEEAVSGVDPE----EARARFEELQKQHDKTTK 238

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
           A  K GY S+   K  + + +     +  A+  E +    R  ++ V + E+ I+++   
Sbjct: 239 ALAKYGYGSKQAEKELSALGDLFKFFKLPARQFEPIYSKARVALDSVRKHERHIMDLCTR 298

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
           +  M R  FIK FP NE N  W+ +  K + +    L R +P ++  QQ+L  ++ +  L
Sbjct: 299 RAQMQRKTFIKEFPGNETNEAWLPDFLKGKVEAPEKLERVLPDVQSAQQQLAQIEAESGL 358

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            L  ++DINR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 359 SLASIKDINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 418

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE
Sbjct: 419 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQE 478

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P +
Sbjct: 479 MGREPTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIISPVE 538

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A    +    +++L  LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 539 SATMEGLMEATREVLAGLTAREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAK 598

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 599 ALRKLR 604


>gi|410625626|ref|ZP_11336402.1| RNA polymerase primary sigma factor [Glaciecola mesophila KMM 241]
 gi|410154836|dbj|GAC23171.1| RNA polymerase primary sigma factor [Glaciecola mesophila KMM 241]
          Length = 612

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/621 (49%), Positives = 420/621 (67%), Gaps = 28/621 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1    MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61   SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121  RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 1057
             +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 181  GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 240

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                 K  + +S      R   K  +++   +R  ++++   E+ +++  V    MP+  
Sbjct: 241  HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRGMMDRIRVQERIVMKHCVTAAKMPKKD 300

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FIK F  NE + +W+            IL  + P ++EL+           K+  ++ + 
Sbjct: 301  FIKAFSGNETSTDWLFE----------ILASDAPYVEELKVHQEELERSIGKMNAVEDET 350

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 351  GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 410

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 411  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 470

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 471  QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 530

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 531  LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 590

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR  +L+ FL+
Sbjct: 591  AKALRKLRHPSRSEQLRSFLD 611



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 410/608 (67%), Gaps = 28/608 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61  SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121 RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 267
            +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 181 GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 240

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
                K  + +S      R   K  +++   +R  ++++   E+ +++  V    MP+  
Sbjct: 241 HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRGMMDRIRVQERIVMKHCVTAAKMPKKD 300

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FIK F  NE + +W+            IL  + P ++EL+           K+  ++ + 
Sbjct: 301 FIKAFSGNETSTDWLFE----------ILASDAPYVEELKVHQEELERSIGKMNAVEDET 350

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 351 GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 410

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 411 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 470

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 471 QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 530

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 531 LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 590

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 591 AKALRKLR 598


>gi|149191850|ref|ZP_01870086.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
 gi|148834326|gb|EDL51327.1| RNA polymerase sigma factor RpoD [Vibrio shilonii AK1]
          Length = 616

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 315/613 (51%), Positives = 415/613 (67%), Gaps = 11/613 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDNNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDVITGFVDPNEEETTAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAFEKEG 1055
              +   +  +E    +   E  +  + E         +L KF+ +   +  ++    + G
Sbjct: 183  IGSELSEADLEDEDDEDVDEDDDSEEEEEDTGIDPELALEKFTALRNSYQDLQLVINEYG 242

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
            Y+S    K+H  +       R T K  + L + LR  +++V   E+ I+   V    MP+
Sbjct: 243  YDSPQVAKSHELVQEVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMRQAVEYGKMPK 302

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              FI VF  NE +  W+D        Y   + R    I+   QKL  ++ +  L + +++
Sbjct: 303  KSFIAVFTGNESSEAWLDEVLASDKPYAEKIKRYEDDIRRSIQKLDIIEEETSLSVQNIK 362

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363  DISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPL 482

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S
Sbjct: 483  PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPVDSATMTS 542

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +R   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543  LRVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 603  HPSRSETLRSFLD 615



 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/600 (51%), Positives = 406/600 (67%), Gaps = 11/600 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LPE+I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPEEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDNNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDVITGFVDPNEEETTAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAFEKEG 265
             +   +  +E    +   E  +  + E         +L KF+ +   +  ++    + G
Sbjct: 183 IGSELSEADLEDEDDEDVDEDDDSEEEEEDTGIDPELALEKFTALRNSYQDLQLVINEYG 242

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
           Y+S    K+H  +       R T K  + L + LR  +++V   E+ I+   V    MP+
Sbjct: 243 YDSPQVAKSHELVQEVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMRQAVEYGKMPK 302

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             FI VF  NE +  W+D        Y   + R    I+   QKL  ++ +  L + +++
Sbjct: 303 KSFIAVFTGNESSEAWLDEVLASDKPYAEKIKRYEDDIRRSIQKLDIIEEETSLSVQNIK 362

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 363 DISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 422

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 423 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPL 482

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S
Sbjct: 483 PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPVDSATMTS 542

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +R   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 LRVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|410643649|ref|ZP_11354142.1| RNA polymerase primary sigma factor [Glaciecola chathamensis S18K6]
 gi|410646950|ref|ZP_11357391.1| RNA polymerase primary sigma factor [Glaciecola agarilytica NO2]
 gi|410133451|dbj|GAC05790.1| RNA polymerase primary sigma factor [Glaciecola agarilytica NO2]
 gi|410136729|dbj|GAC12329.1| RNA polymerase primary sigma factor [Glaciecola chathamensis S18K6]
          Length = 612

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/621 (49%), Positives = 422/621 (67%), Gaps = 28/621 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1    MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61   SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121  RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 1057
             +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 181  GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 240

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                 K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 241  HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 300

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 1167
            FIK F  NE + +W+         Y  I+  + P ++EL+           K+  ++ + 
Sbjct: 301  FIKAFSGNETSTDWL---------YE-IMASDAPYVEELKVHQEELERSIGKMNAVEEET 350

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 351  GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 410

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 411  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 470

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 471  QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 530

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 531  LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 590

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR  +L+ FL+
Sbjct: 591  AKALRKLRHPSRSEQLRSFLD 611



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 412/608 (67%), Gaps = 28/608 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L++   T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61  SDELLMQETTTDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121 RIEEGINQVQCSVAEYPEAITYLLDQWDMYEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYN 267
            +   +  +E    D      E  +         E+  KFS +   ++K R     EG +
Sbjct: 181 GSELSEEELEDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKTRDVIASEGRS 240

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
                K  + +S      R   K  +++   +R+ ++++   E+ +++  V    MP+  
Sbjct: 241 HAKSRKEIDELSEIFKEFRLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVAAAKMPKKD 300

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQTDI 377
           FIK F  NE + +W+         Y  I+  + P ++EL+           K+  ++ + 
Sbjct: 301 FIKAFSGNETSTDWL---------YE-IMASDAPYVEELKVHQEELERSIGKMNAVEEET 350

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 351 GLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 410

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 411 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 470

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P
Sbjct: 471 QEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQP 530

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 531 LDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 590

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 591 AKALRKLR 598


>gi|374851086|dbj|BAL54056.1| RNA polymerase primary sigma factor [uncultured gamma
            proteobacterium]
          Length = 600

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/605 (49%), Positives = 410/605 (67%), Gaps = 12/605 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GK +GYLT+SE+ND LP DIID + +E II     M I V E   D 
Sbjct: 4    EQQQSQIKELIARGKMQGYLTYSEVNDHLPSDIIDPDQVEDIIAMINDMGIEVVEEAPDD 63

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
              L+   + SD++      AAL   DS+FGRT DP++MYMREMG+VELLTR+GE+E+AKR
Sbjct: 64   GQLLPDVVVSDEEEAAEVAAALVADDSEFGRTTDPVRMYMREMGTVELLTREGELELAKR 123

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN-- 1004
            IEEG   +  A+S  P  +   +   +++   + K+ + +   I+ +    + + + +  
Sbjct: 124  IEEGQNQVAEALSRFPKVVEHFIHCFEQVVNGQAKVTDFISDFIEASGLDEDEIEEDDLL 183

Query: 1005 -KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              N ++ +I+ ES   DL          E   K   +   + ++    ++ GY  +   +
Sbjct: 184  VANEDDAEIIAESKGPDLE---------EVKAKLELVKTRYQEVLNCLKQYGYEDKRTQE 234

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A+  ++   +  R T +  ++L + L   + ++ Q EK+IL++ V +  MPR  FI+ F 
Sbjct: 235  AYAGLAEIFMEFRRTPQFFKELTEILAAVVAEIRQEEKRILDLCVKQAQMPRKLFIETFV 294

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             +E +  W+++       Y   L      I+  Q +L+ ++    L ++ ++DINR++  
Sbjct: 295  GHETDPQWLESHLNSGEPYAEALKACADEIRRAQSRLLAIEQANYLSIDQIKDINRRVSI 354

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 355  GEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 414

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +M
Sbjct: 415  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELARRM 474

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED   ++P +AA    +R  ++++
Sbjct: 475  DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSKAMSPVEAATIEGLREAMQNV 534

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 535  LSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 594

Query: 1424 KIFLE 1428
            + FLE
Sbjct: 595  RSFLE 599



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 292/592 (49%), Positives = 401/592 (67%), Gaps = 12/592 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GK +GYLT+SE+ND LP DIID + +E II     M I V E   D 
Sbjct: 4   EQQQSQIKELIARGKMQGYLTYSEVNDHLPSDIIDPDQVEDIIAMINDMGIEVVEEAPDD 63

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
             L+   + SD++      AAL   DS+FGRT DP++MYMREMG+VELLTR+GE+E+AKR
Sbjct: 64  GQLLPDVVVSDEEEAAEVAAALVADDSEFGRTTDPVRMYMREMGTVELLTREGELELAKR 123

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN-- 214
           IEEG   +  A+S  P  +   +   +++   + K+ + +   I+ +    + + + +  
Sbjct: 124 IEEGQNQVAEALSRFPKVVEHFIHCFEQVVNGQAKVTDFISDFIEASGLDEDEIEEDDLL 183

Query: 215 -KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
             N ++ +I+ ES   DL          E   K   +   + ++    ++ GY  +   +
Sbjct: 184 VANEDDAEIIAESKGPDLE---------EVKAKLELVKTRYQEVLNCLKQYGYEDKRTQE 234

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A+  ++   +  R T +  ++L + L   + ++ Q EK+IL++ V +  MPR  FI+ F 
Sbjct: 235 AYAGLAEIFMEFRRTPQFFKELTEILAAVVAEIRQEEKRILDLCVKQAQMPRKLFIETFV 294

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            +E +  W+++       Y   L      I+  Q +L+ ++    L ++ ++DINR++  
Sbjct: 295 GHETDPQWLESHLNSGEPYAEALKACADEIRRAQSRLLAIEQANYLSIDQIKDINRRVSI 354

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 355 GEAKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 414

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +M
Sbjct: 415 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELARRM 474

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED   ++P +AA    +R  ++++
Sbjct: 475 DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSKAMSPVEAATIEGLREAMQNV 534

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 535 LSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 586


>gi|385870288|gb|AFI88808.1| RNA polymerase sigma factor [Pectobacterium sp. SCC3193]
          Length = 611

 Score =  577 bits (1488), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 307/608 (50%), Positives = 419/608 (68%), Gaps = 6/608 (0%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 1001
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
             G++ ++EE    +    +   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183  VGSELSSEEISDDDEEEDEDEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243  AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303  MFTGNETNNSWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMI+TINK++RISRQ+LQE G EP P  +A
Sbjct: 423  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIDTINKLNRISRQMLQEMGREPTPEELA 482

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483  ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 543  HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 602

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 603  EVLRSFLD 610



 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 300/595 (50%), Positives = 410/595 (68%), Gaps = 6/595 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDIID + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIIDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAENTNDADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI 211
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +       
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGESRLSDLIIGFVDPNAEEDIAPTATH 182

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSES 270
            G++ ++EE    +    +   E    +  E +  KF+ +   ++  R+  +  G +   
Sbjct: 183 VGSELSSEEISDDDEEEDEDEEEDDNSIDPELAREKFTELREQYETTRQVIKAHGRSHAL 242

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +   N+S      R   K  + L +++R+ +++V   E+ I+++ V +C MP+ +F+ 
Sbjct: 243 AAQEILNLSEVFKQFRLVPKQFDFLVNSMRSMMDRVRTQERLIIKLCVEQCKMPKKNFVT 302

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N +W      +   ++  L      +    QKL  ++ +  L +  ++DINR+
Sbjct: 303 MFTGNETNNSWFAAAVAMGKPWSEKLNDVEEDVTRSLQKLQQIEEETGLTIEQVKDINRR 362

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 363 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 422

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMI+TINK++RISRQ+LQE G EP P  +A
Sbjct: 423 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIDTINKLNRISRQMLQEMGREPTPEELA 482

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+RS  
Sbjct: 483 ERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLRSAT 542

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|373948591|ref|ZP_09608552.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|378707586|ref|YP_005272480.1| RNA polymerase sigma-70 subunit RpoD [Shewanella baltica OS678]
 gi|386325567|ref|YP_006021684.1| RNA polymerase sigma-70 subunit RpoD [Shewanella baltica BA175]
 gi|418023210|ref|ZP_12662195.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS625]
 gi|315266575|gb|ADT93428.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS678]
 gi|333819712|gb|AEG12378.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|353537093|gb|EHC06650.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS625]
 gi|373885191|gb|EHQ14083.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
          Length = 611

 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 417/612 (68%), Gaps = 24/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
             +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 188  LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 247

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 248  FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 307

Query: 1126 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308  ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479  EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 539  KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 598

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 599  PSRSEILKSFLD 610



 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 408/599 (68%), Gaps = 24/599 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
            +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 188 LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 247

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 248 FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 307

Query: 336 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308 ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479 EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 539 KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|423702574|ref|ZP_17677006.1| RNA polymerase sigma factor rpoD [Escherichia coli H730]
 gi|385710066|gb|EIG47058.1| RNA polymerase sigma factor rpoD [Escherichia coli H730]
          Length = 613

 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV+KFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVNKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV+KFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVNKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|419274417|ref|ZP_13816707.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10D]
 gi|378114142|gb|EHW75699.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10D]
          Length = 613

 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+N+ LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNNHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+N+ LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNNHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|407698882|ref|YP_006823669.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Black Sea
            11']
 gi|407248029|gb|AFT77214.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Black Sea
            11']
          Length = 610

 Score =  577 bits (1486), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 308/602 (51%), Positives = 408/602 (67%), Gaps = 5/602 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8    QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
                +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68   QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 1007
              +  +++  P  I  +L   D     EI++ +I+ G +D N     +     +    + 
Sbjct: 128  NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDDQDLAPTATHVGSELSE 187

Query: 1008 NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
             E     +    + S E    +  E +  +F+     + K R+  EK+G          N
Sbjct: 188  EELDDEDDDEDDEDSDEDDSGVDPELARERFTEPREQYLKTREVIEKKGRAHADSRAQIN 247

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +S+     R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F  NE
Sbjct: 248  ALSDVFKEFRLVPKQFDRMVKNMREMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGNE 307

Query: 1127 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 1186
             +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  GE 
Sbjct: 308  TSNAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSIGEA 367

Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 368  KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 427

Query: 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306
            ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M MP
Sbjct: 428  ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMP 487

Query: 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 1366
            E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L  
Sbjct: 488  EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEVLAG 547

Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ F
Sbjct: 548  LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSF 607

Query: 1427 LE 1428
            L+
Sbjct: 608  LD 609



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 301/589 (51%), Positives = 398/589 (67%), Gaps = 5/589 (0%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D + L++
Sbjct: 8   QIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVSESAPDADELLM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
               +D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68  QEANADEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNKNN 217
             +  +++  P  I  +L   D     EI++ +I+ G +D N     +     +    + 
Sbjct: 128 NQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIISGFVDPNDDQDLAPTATHVGSELSE 187

Query: 218 NEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
            E     +    + S E    +  E +  +F+     + K R+  EK+G          N
Sbjct: 188 EELDDEDDDEDDEDSDEDDSGVDPELARERFTEPREQYLKTREVIEKKGRAHADSRAQIN 247

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +S+     R   K  +++   +R  +++V   E+ +++  V    MP+  FIK F  NE
Sbjct: 248 ALSDVFKEFRLVPKQFDRMVKNMREMMDKVRIQERLVMKFCVVNAKMPKKDFIKAFAGNE 307

Query: 337 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 396
            +  W+    K    Y   L  N   I+    K+  ++ +  L + D++DINR+M  GE 
Sbjct: 308 TSNAWLHEAVKSGAPYAADLAVNQEEIERCISKMNQVEQETGLVIADIKDINRRMSIGEA 367

Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
           KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 368 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 427

Query: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 516
           ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M MP
Sbjct: 428 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMP 487

Query: 517 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 576
           E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L  
Sbjct: 488 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKDATQEVLAG 547

Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 596


>gi|266618720|pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
            Activator-Dependent Transcription Initiation Complex
          Length = 613

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   +++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   +++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|53802939|ref|YP_115383.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
 gi|53756700|gb|AAU90991.1| RNA polymerase sigma-70 factor [Methylococcus capsulatus str. Bath]
          Length = 599

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/606 (50%), Positives = 407/606 (67%), Gaps = 16/606 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  GK +GYLTFSE+ND LP DI+D E +E II     M I V E V D 
Sbjct: 4    EQQQHQLKELIAKGKMQGYLTFSEVNDHLPSDIVDPEQMEDIICMINDMGIEVHEDVPDN 63

Query: 887  ETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            E L+        + +D+  E   A  S+VD++ GRT DP++MYMREMG+VELLTR+GE+ 
Sbjct: 64   EDLIQDTAVVAESDEDEAAEVAAALASSVDTELGRTTDPVRMYMREMGTVELLTREGELS 123

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEGL    + +   P  +   L A + +   E+++ +++    D   +       
Sbjct: 124  IAKRIEEGLNIAANELVRFPAAMEHFLKAFETVDNGELRLSDLISDFFDPAAADT----V 179

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
              +++ E +I+ E  +      +L K K  +  K    +        A  K GY  E   
Sbjct: 180  ATEDDAEAEIIDEGDTG--PDPELVKEKLAAFRKLHKAAV------TAHHKYGYGHEKTQ 231

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            K+ + ++   +  + T +  ++L DTLR+ + ++ + E+ + +I V K  MP+  FI+ F
Sbjct: 232  KSFDALATAFMEFKKTPQFFKELTDTLRDTVAKIREQERALTDICVTKGKMPKAEFIESF 291

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              +E +  W+D        Y   +  +   I+ +Q KL  ++ +  L +  ++DI+R++ 
Sbjct: 292  SGSETDEGWLDRVCDPAKPYAAAIKAHAEEIRRIQAKLAQIEKENRLDIALIKDIHRRVS 351

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
            AGE +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 352  AGENQARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 412  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPDELAAR 471

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M+MPE+K+RK+MKIAKEP+SME+P+GDD+DSHLGDFIED  +L+P + A  AS+R   + 
Sbjct: 472  MDMPEDKVRKVMKIAKEPISMETPIGDDDDSHLGDFIEDSRVLSPVEHATVASLRETTQQ 531

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +
Sbjct: 532  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 591

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 592  LRSFLD 597



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/593 (50%), Positives = 397/593 (66%), Gaps = 16/593 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  GK +GYLTFSE+ND LP DI+D E +E II     M I V E V D 
Sbjct: 4   EQQQHQLKELIAKGKMQGYLTFSEVNDHLPSDIVDPEQMEDIICMINDMGIEVHEDVPDN 63

Query: 97  ETLMLSNI----TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           E L+        + +D+  E   A  S+VD++ GRT DP++MYMREMG+VELLTR+GE+ 
Sbjct: 64  EDLIQDTAVVAESDEDEAAEVAAALASSVDTELGRTTDPVRMYMREMGTVELLTREGELS 123

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEGL    + +   P  +   L A + +   E+++ +++    D   +       
Sbjct: 124 IAKRIEEGLNIAANELVRFPAAMEHFLKAFETVDNGELRLSDLISDFFDPAAADT----V 179

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
             +++ E +I+ E  +      +L K K  +  K    +        A  K GY  E   
Sbjct: 180 ATEDDAEAEIIDEGDTG--PDPELVKEKLAAFRKLHKAAV------TAHHKYGYGHEKTQ 231

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           K+ + ++   +  + T +  ++L DTLR+ + ++ + E+ + +I V K  MP+  FI+ F
Sbjct: 232 KSFDALATAFMEFKKTPQFFKELTDTLRDTVAKIREQERALTDICVTKGKMPKAEFIESF 291

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             +E +  W+D        Y   +  +   I+ +Q KL  ++ +  L +  ++DI+R++ 
Sbjct: 292 SGSETDEGWLDRVCDPAKPYAAAIKAHAEEIRRIQAKLAQIEKENRLDIALIKDIHRRVS 351

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
           AGE +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 352 AGENQARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 412 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPDELAAR 471

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M+MPE+K+RK+MKIAKEP+SME+P+GDD+DSHLGDFIED  +L+P + A  AS+R   + 
Sbjct: 472 MDMPEDKVRKVMKIAKEPISMETPIGDDDDSHLGDFIEDSRVLSPVEHATVASLRETTQQ 531

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 532 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|257454210|ref|ZP_05619480.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
 gi|257448383|gb|EEV23356.1| RNA polymerase sigma factor RpoD [Enhydrobacter aerosaccus SK60]
          Length = 634

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 302/631 (47%), Positives = 423/631 (67%), Gaps = 30/631 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+   +   LI+LGKE+GYLT++EIND LPE + + + I+ II+    + I + E   D 
Sbjct: 3    EHSTSQLATLIQLGKEQGYLTYAEINDQLPESVTESDQIDDIIQMLTDVGIKIFETAPDE 62

Query: 887  ETLMLSNITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + +MLS+   DD+  V+EA  A L++V+S+ GRT DP++MYMREMG+V+LLTR+GEI IA
Sbjct: 63   DDIMLSDDADDDEIAVDEAA-AVLASVESEPGRTTDPVRMYMREMGTVDLLTREGEIAIA 121

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------------- 991
            KRIE+G++D+ HA++  P T+  ++    +  + E KI +I+ G +D             
Sbjct: 122  KRIEDGIRDVQHAMTFWPGTVAMLINEYRQTFEGEKKISDIITGFLDPEAADVIPLADDE 181

Query: 992  -------------KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL-IKF 1037
                         K+ ++ + +    +N +E +      S D  TE+   L  E + ++F
Sbjct: 182  EVEIALPIIKPKVKDDTAEDELDDEAENADEIEEADGEVSEDADTEEASGLDPEEVRLRF 241

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
              +   F K++        +SE    A N ++N  +  +  ++  + + D +R     V 
Sbjct: 242  EELEQLFTKVKDLLATHDRDSEVVKTAMNELANCFMLFKLNSRVSDNIMDMMREVYEDVR 301

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
            + E+ I+++V+ +  MP+  F K FP NE NL+W+ N    +  +   L R +  + + Q
Sbjct: 302  KNERHIMKLVIRRGKMPKDEFRKTFPHNETNLDWLPNRIAGKPAFADTLERVLDEVLQYQ 361

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             ++   + ++ + ++ ++ + R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 362  GRIQQHEQNLGMSIDQMKVVARNMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 421

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 422  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 481

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            KI+R+SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 482  KINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGD 541

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED ++ +P D A    ++   +++L +LT RE+KVL+MRFGI+MS+DHTLEEVGKQFD
Sbjct: 542  FIEDSSISSPVDEATAQGLKEATREVLANLTEREAKVLKMRFGIDMSTDHTLEEVGKQFD 601

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 602  VTRERIRQIEAKALRKLRHPSRSEHLRSFLE 632



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 294/618 (47%), Positives = 414/618 (66%), Gaps = 30/618 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+   +   LI+LGKE+GYLT++EIND LPE + + + I+ II+    + I + E   D 
Sbjct: 3   EHSTSQLATLIQLGKEQGYLTYAEINDQLPESVTESDQIDDIIQMLTDVGIKIFETAPDE 62

Query: 97  ETLMLSNITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + +MLS+   DD+  V+EA  A L++V+S+ GRT DP++MYMREMG+V+LLTR+GEI IA
Sbjct: 63  DDIMLSDDADDDEIAVDEAA-AVLASVESEPGRTTDPVRMYMREMGTVDLLTREGEIAIA 121

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------------- 201
           KRIE+G++D+ HA++  P T+  ++    +  + E KI +I+ G +D             
Sbjct: 122 KRIEDGIRDVQHAMTFWPGTVAMLINEYRQTFEGEKKISDIITGFLDPEAADVIPLADDE 181

Query: 202 -------------KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL-IKF 247
                        K+ ++ + +    +N +E +      S D  TE+   L  E + ++F
Sbjct: 182 EVEIALPIIKPKVKDDTAEDELDDEAENADEIEEADGEVSEDADTEEASGLDPEEVRLRF 241

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
             +   F K++        +SE    A N ++N  +  +  ++  + + D +R     V 
Sbjct: 242 EELEQLFTKVKDLLATHDRDSEVVKTAMNELANCFMLFKLNSRVSDNIMDMMREVYEDVR 301

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
           + E+ I+++V+ +  MP+  F K FP NE NL+W+ N    +  +   L R +  + + Q
Sbjct: 302 KNERHIMKLVIRRGKMPKDEFRKTFPHNETNLDWLPNRIAGKPAFADTLERVLDEVLQYQ 361

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            ++   + ++ + ++ ++ + R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 362 GRIQQHEQNLGMSIDQMKVVARNMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 421

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 422 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 481

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           KI+R+SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 482 KINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGD 541

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED ++ +P D A    ++   +++L +LT RE+KVL+MRFGI+MS+DHTLEEVGKQFD
Sbjct: 542 FIEDSSISSPVDEATAQGLKEATREVLANLTEREAKVLKMRFGIDMSTDHTLEEVGKQFD 601

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 602 VTRERIRQIEAKALRKLR 619


>gi|254517369|ref|ZP_05129426.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
 gi|219674207|gb|EED30576.1| RNA polymerase sigma factor RpoD [gamma proteobacterium NOR5-3]
          Length = 607

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/601 (50%), Positives = 413/601 (68%), Gaps = 10/601 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D + L+L
Sbjct: 10   RLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLIL 69

Query: 892  SNI--TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            ++   ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNN 1007
            G+++++ A++  P  +  +L     ++K E K+ +I+ G ++   +  S  ++ +     
Sbjct: 130  GIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADILVGYLNPADHVPSAQQIAEQQAAK 189

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                +  + + +    + +E  K     +F+ +   F+K  K   ++G   ++ IK    
Sbjct: 190  AAGNVDEDDNDSPAGPDPVEAKK-----RFTALKRQFNKTEKILLEKGRQDKAAIKEMEK 244

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            +       +FT K  + L D  R+ +  V + E++I+ + V +C MPR  FI  F  NE 
Sbjct: 245  LGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRLAVRRCQMPRKDFITSFQGNES 304

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            N  W+   T+ + DY   L      I   Q+++  ++    L + ++++INR+M  GE +
Sbjct: 305  NAKWLSRHTR-KKDYGPKLNAYKEEILRAQRQIGQIEAATGLTVTEIKEINRRMSMGEAR 363

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 364  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 423

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 424  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 483

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P DAA    +    KD+L  L
Sbjct: 484  DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTINSPIDAATGQGLMEATKDVLAGL 543

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL
Sbjct: 544  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFL 603

Query: 1428 E 1428
            +
Sbjct: 604  D 604



 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 301/596 (50%), Positives = 408/596 (68%), Gaps = 11/596 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II+    M I V E   D + L+L
Sbjct: 10  RLKSLIAKGKEQGYLTYAEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEQAPDADDLIL 69

Query: 102 SNI--TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           ++   ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TDGDGSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNN 217
           G+++++ A++  P  +  +L     ++K E K+ +I+ G ++   +  S  ++ +     
Sbjct: 130 GIRELMAALAFYPGAVKSVLDDYALVAKEEKKLADILVGYLNPADHVPSAQQIAEQQAAK 189

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
               +  + + +    + +E  K     +F+ +   F+K  K   ++G   ++ IK    
Sbjct: 190 AAGNVDEDDNDSPAGPDPVEAKK-----RFTALKRQFNKTEKILLEKGRQDKAAIKEMEK 244

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           +       +FT K  + L D  R+ +  V + E++I+ + V +C MPR  FI  F  NE 
Sbjct: 245 LGEIFKFFKFTPKVFDPLNDEARSALAGVREQEREIMRLAVRRCQMPRKDFITSFQGNES 304

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           N  W+   T+ + DY   L      I   Q+++  ++    L + ++++INR+M  GE +
Sbjct: 305 NAKWLSRHTR-KKDYGPKLNAYKEEILRAQRQIGQIEAATGLTVTEIKEINRRMSMGEAR 363

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 364 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 423

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMPE
Sbjct: 424 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPE 483

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P DAA    +    KD+L  L
Sbjct: 484 DKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTINSPIDAATGQGLMEATKDVLAGL 543

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D+L
Sbjct: 544 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYL 599


>gi|262167116|ref|ZP_06034830.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
 gi|262024416|gb|EEY43103.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC27]
          Length = 621

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 319/625 (51%), Positives = 420/625 (67%), Gaps = 30/625 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 1043
                   I  E S ADL+ E    ++ E                        KF+ +   
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGK 235

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   E+ +
Sbjct: 236  FQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLV 295

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            ++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QKL  +
Sbjct: 296  MKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMI 355

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 356  EQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 415

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 416  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 475

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 476  RQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 535

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 536  LELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 595

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RQIEAKALRKLRHPSRSEVLRSFLD 620



 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 312/612 (50%), Positives = 411/612 (67%), Gaps = 30/612 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 253
                  I  E S ADL+ E    ++ E                        KF+ +   
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGK 235

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   E+ +
Sbjct: 236 FQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLV 295

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           ++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QKL  +
Sbjct: 296 MKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMI 355

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 356 EQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 415

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 416 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 475

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 476 RQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 535

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 536 LELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 595

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 596 RQIEAKALRKLR 607


>gi|71730361|gb|EAO32443.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
            region 4:Sigma-70, non-essential region:Sigma-70 region
            1.2 [Xylella fastidiosa Ann-1]
          Length = 623

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 412/607 (67%), Gaps = 13/607 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 891
             K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17   IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 892  ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77   EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 137  EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEEDNSVTSAVDV 194

Query: 1007 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 195  TDESIVEVDEEDDDSVGNDEDAPMIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 254

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 255  IKVREDVAAIFVTFKLSLPLTDLLVQQLQNTVNSVKDHERKVLHLATNVAKMPRKDFIRS 314

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 315  WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMM 374

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
            + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 375  VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 434

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 435  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 494

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 495  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 554

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 555  EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 614

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 615  QLRSFLD 621



 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/594 (51%), Positives = 402/594 (67%), Gaps = 13/594 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 101
            K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17  IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 102 ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77  EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 137 EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEEDNSVTSAVDV 194

Query: 217 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 195 TDESIVEVDEEDDDSVGNDEDAPMIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 254

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 255 IKVREDVAAIFVTFKLSLPLTDLLVQQLQNTVNSVKDHERKVLHLATNVAKMPRKDFIRS 314

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 315 WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMM 374

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
           + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 375 VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 434

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 435 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 494

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 495 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 554

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608


>gi|386340136|ref|YP_006036502.1| RNA polymerase sigma-70 subunit RpoD [Shewanella baltica OS117]
 gi|334862537|gb|AEH13008.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS117]
          Length = 611

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 417/612 (68%), Gaps = 24/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
             +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 188  LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 247

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 248  FEIGEIFKEFRLVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 307

Query: 1126 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308  ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479  EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 539  KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 598

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 599  PSRSEILKSFLD 610



 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 408/599 (68%), Gaps = 24/599 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
            +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 188 LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 247

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 248 FEIGEIFKEFRLVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 307

Query: 336 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308 ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479 EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 539 KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|152995072|ref|YP_001339907.1| RNA polymerase sigma-70 subunit RpoD [Marinomonas sp. MWYL1]
 gi|150835996|gb|ABR69972.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas sp. MWYL1]
          Length = 612

 Score =  576 bits (1485), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/606 (50%), Positives = 414/606 (68%), Gaps = 11/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LP+D+ D E +E II     M I+VSE   D ++L++
Sbjct: 8    RLKELISKGKEQGYLTYAEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEVAPDKDSLLM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
                 +D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68   EEGDATDEAAAEEAAAALAAVEGDITRTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFSSNNRVIK 1002
             ++++ AIS  P  +  +L A  K+ + E ++ +I  G ID        ++ ++   +I 
Sbjct: 128  TREVMAAISYFPGAVDVLLDAYAKVQEEEGRLSDIFSGFIDGDGEEPVFEDVATEEPIID 187

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
             +  +++E      ++ + +    +    E+ ++F++I+  + ++++  E       +  
Sbjct: 188  EDTVDSDEDDDDSDTAEEETDNGPDP--EETALRFNDITRIYTELKELLETRNRQDPAVQ 245

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
                 +S     I+   K  + L D +R+++ +V + E+ I+++ V K GMPR  F+K F
Sbjct: 246  SKQEELSISFAPIKLVPKLFDDLVDRVRSRMEKVREQERLIMQVCVRKSGMPRTEFLKRF 305

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE N +W+  +     DY   L  N       Q+KL  +  +  L + +L++INR++ 
Sbjct: 306  PSNETNSDWLKEQIASGADYAATLEENEAEFMRSQRKLRAVSKETGLTIAELKEINRRIS 365

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 366  IGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +
Sbjct: 426  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAAR 485

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A    +R     
Sbjct: 486  MDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIEGLRESTTM 545

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 546  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEH 605

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 606  LRSFLD 611



 Score =  561 bits (1446), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/593 (50%), Positives = 405/593 (68%), Gaps = 11/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LP+D+ D E +E II     M I+VSE   D ++L++
Sbjct: 8   RLKELISKGKEQGYLTYAEVNDHLPDDLSDPEQVEEIIAMINDMGITVSEVAPDKDSLLM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
                +D+   E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68  EEGDATDEAAAEEAAAALAAVEGDITRTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFSSNNRVIK 212
            ++++ AIS  P  +  +L A  K+ + E ++ +I  G ID        ++ ++   +I 
Sbjct: 128 TREVMAAISYFPGAVDVLLDAYAKVQEEEGRLSDIFSGFIDGDGEEPVFEDVATEEPIID 187

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
            +  +++E      ++ + +    +    E+ ++F++I+  + ++++  E       +  
Sbjct: 188 EDTVDSDEDDDDSDTAEEETDNGPDP--EETALRFNDITRIYTELKELLETRNRQDPAVQ 245

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
                +S     I+   K  + L D +R+++ +V + E+ I+++ V K GMPR  F+K F
Sbjct: 246 SKQEELSISFAPIKLVPKLFDDLVDRVRSRMEKVREQERLIMQVCVRKSGMPRTEFLKRF 305

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE N +W+  +     DY   L  N       Q+KL  +  +  L + +L++INR++ 
Sbjct: 306 PSNETNSDWLKEQIASGADYAATLEENEAEFMRSQRKLRAVSKETGLTIAELKEINRRIS 365

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 366 IGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAAR 485

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A    +R     
Sbjct: 486 MDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPIDIATIEGLRESTTM 545

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 546 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|16130963|ref|NP_417539.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K-12
            substr. MG1655]
 gi|170082610|ref|YP_001731930.1| RNA polymerase sigma factor RpoD [Escherichia coli str. K-12 substr.
            DH10B]
 gi|238902178|ref|YP_002927974.1| RNA polymerase sigma factor RpoD [Escherichia coli BW2952]
 gi|386594209|ref|YP_006090609.1| RNA polymerase sigma-70 subunit RpoD [Escherichia coli DH1]
 gi|387622736|ref|YP_006130364.1| RNA polymerase sigma factor RpoD [Escherichia coli DH1]
 gi|388479067|ref|YP_491259.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K-12
            substr. W3110]
 gi|417946933|ref|ZP_12590139.1| RNA polymerase sigma factor RpoD [Escherichia coli XH140A]
 gi|417977599|ref|ZP_12618381.1| RNA polymerase sigma factor RpoD [Escherichia coli XH001]
 gi|418956550|ref|ZP_13508475.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli J53]
 gi|450250149|ref|ZP_21901544.1| RNA polymerase sigma factor RpoD [Escherichia coli S17]
 gi|1710680|sp|P00579.2|RPOD_ECOLI RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|448262658|pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
            Holoenzyme
 gi|448262664|pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
            Holoenzyme
 gi|882590|gb|AAA89147.1| CG Site No. 231; alternate gene name alt [Escherichia coli str. K-12
            substr. MG1655]
 gi|1789448|gb|AAC76103.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K-12
            substr. MG1655]
 gi|73671318|gb|AAZ80070.1| RpoD [Escherichia coli LW1655F+]
 gi|85675868|dbj|BAE77118.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K12
            substr. W3110]
 gi|169890445|gb|ACB04152.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K-12
            substr. DH10B]
 gi|238863501|gb|ACR65499.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|260447898|gb|ACX38320.1| RNA polymerase, sigma 70 subunit, RpoD [Escherichia coli DH1]
 gi|315137660|dbj|BAJ44819.1| RNA polymerase sigma factor RpoD [Escherichia coli DH1]
 gi|342361321|gb|EGU25462.1| RNA polymerase sigma factor RpoD [Escherichia coli XH140A]
 gi|344192731|gb|EGV46819.1| RNA polymerase sigma factor RpoD [Escherichia coli XH001]
 gi|359333272|dbj|BAL39719.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str. K-12
            substr. MDS42]
 gi|384380344|gb|EIE38210.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli J53]
 gi|449316373|gb|EMD06490.1| RNA polymerase sigma factor RpoD [Escherichia coli S17]
          Length = 613

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|315127802|ref|YP_004069805.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315016316|gb|ADT69654.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 614

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 315/607 (51%), Positives = 415/607 (68%), Gaps = 8/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN-EE 1010
              +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +   E
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDAEEAPPIAATNIGSELSE 187

Query: 1011 KILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            K L +S   D  ++  ++ +        E+ + F N+   + K R+ F+ +G +      
Sbjct: 188  KQLDDSDDDDDDSDDEDEEEVDTGPDPEEARVHFENLRDLYTKARETFDNKGRSHPESQA 247

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F 
Sbjct: 248  AILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFA 307

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  
Sbjct: 308  NNETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSI 367

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M
Sbjct: 428  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERM 487

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+
Sbjct: 488  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDV 547

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 548  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 607

Query: 1424 KIFLEGK 1430
            K FL+ K
Sbjct: 608  KSFLDAK 614



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 309/600 (51%), Positives = 408/600 (68%), Gaps = 9/600 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN-EE 220
             +  +++  P  I  +L   DK    E+++ +I+ G  D +      +   N  +   E
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIISGFFDPDAEEAPPIAATNIGSELSE 187

Query: 221 KILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           K L +S   D  ++  ++ +        E+ + F N+   + K R+ F+ +G +      
Sbjct: 188 KQLDDSDDDDDDSDDEDEEEVDTGPDPEEARVHFENLRDLYTKARETFDNKGRSHPESQA 247

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       +   K  +++ + +R  +++V   E+ I++  V    +P+  F+K F 
Sbjct: 248 AILEIGELFRTFKLVPKQFDRMVNNMREMMDRVRVQERLIMKHAVQVSKLPKKTFVKHFA 307

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE +  W+D E      ++  L    P I     KL +++    L +  ++DINR+M  
Sbjct: 308 NNETDTAWLDIEIAANEKHSAKLEEVKPEILRCISKLTSMEESTGLSIERIKDINRRMSI 367

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A +M
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELAERM 487

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    D+
Sbjct: 488 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPIDSATMESLRGATNDV 547

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 607


>gi|94499953|ref|ZP_01306488.1| RNA polymerase sigma factor [Bermanella marisrubri]
 gi|94427811|gb|EAT12786.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
          Length = 606

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 309/601 (51%), Positives = 415/601 (69%), Gaps = 7/601 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++++ND LP+DI   E +E II+    + I+VSE   D + L +
Sbjct: 8    RLKELIAKGKEQGYLTYAQVNDHLPDDIATPEQVEDIIRMINDIGITVSEVAPDADELNM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
              +T+D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   GEVTTDEAAIEEAAAALAAVETDVGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADK-ISKNEI-KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ A+S  P  +  +L A ++ ++  EI ++ ++ +G ID   +S++        + E
Sbjct: 128  REVMAALSYFPGAVRTVLDAVEESMADEEINRLGDVFNGFID---ASDDDPEPATPVSAE 184

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIK--FSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                 +S   D  +           +K   + I    DK  KA EK G  S+   K    
Sbjct: 185  AAADKDSDDDDDDSSDAPSGPDPEEVKRRMAEIEKQLDKTEKAIEKHGRGSKQADKEGEK 244

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            ++     I+ + K  + L  T R+ ++ +   E+QI+ I   K  M R  FIK F  NE 
Sbjct: 245  LAELFAPIKLSPKYFDDLVGTARDNLDFIRVQERQIMVICTRKAKMKRQEFIKSFQGNEG 304

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            N +W+D+      DY+ I+  +   +K  Q+K+  ++  + L ++D+++INR++  GE +
Sbjct: 305  NDSWIDDLINAGKDYSQIIENHGYDLKRAQKKIRQVKDRVGLEISDIKEINRRVSIGEAR 364

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 365  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 424

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G E  P  +A +M+MPE
Sbjct: 425  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERMDMPE 484

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D A    +    + +L+ L
Sbjct: 485  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNGHSPIDTATETGLTDATRSVLSGL 544

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RESKVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL
Sbjct: 545  TARESKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLRSFL 604

Query: 1428 E 1428
            +
Sbjct: 605  D 605



 Score =  561 bits (1446), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/596 (51%), Positives = 409/596 (68%), Gaps = 8/596 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++++ND LP+DI   E +E II+    + I+VSE   D + L +
Sbjct: 8   RLKELIAKGKEQGYLTYAQVNDHLPDDIATPEQVEDIIRMINDIGITVSEVAPDADELNM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
             +T+D+   E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  GEVTTDEAAIEEAAAALAAVETDVGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADK-ISKNEI-KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ A+S  P  +  +L A ++ ++  EI ++ ++ +G ID   +S++        + E
Sbjct: 128 REVMAALSYFPGAVRTVLDAVEESMADEEINRLGDVFNGFID---ASDDDPEPATPVSAE 184

Query: 220 EKILIESSSADLSTEQLEKLKYESLIK--FSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
                +S   D  +           +K   + I    DK  KA EK G  S+   K    
Sbjct: 185 AAADKDSDDDDDDSSDAPSGPDPEEVKRRMAEIEKQLDKTEKAIEKHGRGSKQADKEGEK 244

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           ++     I+ + K  + L  T R+ ++ +   E+QI+ I   K  M R  FIK F  NE 
Sbjct: 245 LAELFAPIKLSPKYFDDLVGTARDNLDFIRVQERQIMVICTRKAKMKRQEFIKSFQGNEG 304

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           N +W+D+      DY+ I+  +   +K  Q+K+  ++  + L ++D+++INR++  GE +
Sbjct: 305 NDSWIDDLINAGKDYSQIIENHGYDLKRAQKKIRQVKDRVGLEISDIKEINRRVSIGEAR 364

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 365 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 424

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G E  P  +A +M+MPE
Sbjct: 425 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREATPEELAERMDMPE 484

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N  +P D A    +    + +L+ L
Sbjct: 485 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVNGHSPIDTATETGLTDATRSVLSGL 544

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           T RESKVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 545 TARESKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHL 600


>gi|418464176|ref|ZP_13035117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans RhAA1]
 gi|359757356|gb|EHK91511.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans RhAA1]
          Length = 616

 Score =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/617 (49%), Positives = 414/617 (67%), Gaps = 19/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNMLSESETEELAE 181

Query: 1006 NNNEEK--------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
            + N E+                + S  +D       ++  E   KF+ +     K  ++ 
Sbjct: 182  DFNSEEGGDIDNEHEEEEDNEEVSSDDSDSDNSIDPEIARE---KFTALKQQHQKTLESI 238

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             K G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV   
Sbjct: 239  AKHGRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRSQERFIQRIVVENA 298

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +
Sbjct: 299  KMPKSGFQKSFIGHETADTWLVKALSAGKSWSEKLVQYESQLRQAITNLVQIEQDTHLTI 358

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359  PQIREIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A
Sbjct: 479  REASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSA 538

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539  TVQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 599  RKLRHPSRSETLRSFLD 615



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/604 (49%), Positives = 405/604 (67%), Gaps = 19/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNMLSESETEELAE 181

Query: 216 NNNEEK--------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
           + N E+                + S  +D       ++  E   KF+ +     K  ++ 
Sbjct: 182 DFNSEEGGDIDNEHEEEEDNEEVSSDDSDSDNSIDPEIARE---KFTALKQQHQKTLESI 238

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            K G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV   
Sbjct: 239 AKHGRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRSQERFIQRIVVENA 298

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +
Sbjct: 299 KMPKSGFQKSFIGHETADTWLVKALSAGKSWSEKLVQYESQLRQAITNLVQIEQDTHLTI 358

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359 PQIREIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A
Sbjct: 479 REASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSA 538

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539 TVQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 622 RKLR 625
           RKLR
Sbjct: 599 RKLR 602


>gi|419939445|ref|ZP_14456236.1| RNA polymerase sigma factor RpoD [Escherichia coli 75]
 gi|388407239|gb|EIL67612.1| RNA polymerase sigma factor RpoD [Escherichia coli 75]
          Length = 613

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 412/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI D  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIGDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 403/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI D  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIGDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|110834924|ref|YP_693783.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
 gi|110648035|emb|CAL17511.1| RNA polymerase sigma factor RpoD [Alcanivorax borkumensis SK2]
          Length = 633

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/625 (48%), Positives = 415/625 (66%), Gaps = 41/625 (6%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 894
            I LGKE+GYLT++E+ND LP+ I D + +E II+    M I+V E   D + L +  S  
Sbjct: 16   IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            ++D+   E   A L++V+++ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76   STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN------ 1008
            +HA++  P  +  ++    ++   E K+ +I+ G +D N   ++     N N +      
Sbjct: 136  LHALAFWPGAVDMVIEEYARVENEERKLTDIIAGYLDPN---DDGAAATNANRDPAFAEK 192

Query: 1009 ----------------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 1046
                                  ++    +          L   ++E+L K        +K
Sbjct: 193  AKKAAEEKAKAKEKAKEEGSDDKDSDDEDEEDEGGLDPVLAAERFETLKKLQ------EK 246

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
              ++ ++ G +  S  KA   ++      +   +  + +    R+ ++ V + E+QI+  
Sbjct: 247  AERSLKRNGRDHASTAKALEALAEHFTLFKLVPRIFDSMLVGARDNLDLVRKFERQIMSA 306

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLI--LCRNIPSIKELQQKLINLQ 1164
             + + GM R  FIK FP NE N+ W+D++ K +    +   L      ++  Q+K+  ++
Sbjct: 307  TIRRGGMDRKDFIKAFPGNETNMEWIDSQLKTKKGKAIADKLSVVKEDVQRAQRKISTIE 366

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
              I LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 367  DIIGLPVADIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 426

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ R
Sbjct: 427  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQR 486

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM
Sbjct: 487  QMLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNM 546

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
             +P D+A +  +    +D+L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 547  ESPVDSATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 606

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLEG 1429
            QIEAKALRKLRHPSR   L+ FL+G
Sbjct: 607  QIEAKALRKLRHPSRSEHLRSFLDG 631



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 292/611 (47%), Positives = 405/611 (66%), Gaps = 41/611 (6%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 104
           I LGKE+GYLT++E+ND LP+ I D + +E II+    M I+V E   D + L +  S  
Sbjct: 16  IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           ++D+   E   A L++V+++ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76  STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN------ 218
           +HA++  P  +  ++    ++   E K+ +I+ G +D N   ++     N N +      
Sbjct: 136 LHALAFWPGAVDMVIEEYARVENEERKLTDIIAGYLDPN---DDGAAATNANRDPAFAEK 192

Query: 219 ----------------------EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK 256
                                 ++    +          L   ++E+L K        +K
Sbjct: 193 AKKAAEEKAKAKEKAKEEGSDDKDSDDEDEEDEGGLDPVLAAERFETLKKLQ------EK 246

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
             ++ ++ G +  S  KA   ++      +   +  + +    R+ ++ V + E+QI+  
Sbjct: 247 AERSLKRNGRDHASTAKALEALAEHFTLFKLVPRIFDSMLVGARDNLDLVRKFERQIMSA 306

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLI--LCRNIPSIKELQQKLINLQ 374
            + + GM R  FIK FP NE N+ W+D++ K +    +   L      ++  Q+K+  ++
Sbjct: 307 TIRRGGMDRKDFIKAFPGNETNMEWIDSQLKTKKGKAIADKLSVVKEDVQRAQRKISTIE 366

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
             I LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 367 DIIGLPVADIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 426

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ R
Sbjct: 427 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQR 486

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM
Sbjct: 487 QMLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNM 546

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
            +P D+A +  +    +D+L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 547 ESPVDSATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 606

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 607 QIEAKALRKLR 617


>gi|386084679|ref|YP_006000961.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa subsp.
            fastidiosa GB514]
 gi|32130003|sp|Q87DT7.1|RPOD_XYLFT RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|307579626|gb|ADN63595.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa subsp.
            fastidiosa GB514]
          Length = 618

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 313/618 (50%), Positives = 421/618 (68%), Gaps = 35/618 (5%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 891
             K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 12   IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 71

Query: 892  ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDG---LIDKNFSSNNRVIKG 1003
            EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G   LI+++ S  + V   
Sbjct: 132  EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDLIEEDNSVTSSVDVT 190

Query: 1004 NKN-------------NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
            +++             N+E+  +I    A++++            +  ++S  + K +K 
Sbjct: 191  DESIVEVDEEDDDSVGNDEDAPMIGPDPAEVAS------------RIESLSTEYAKFKKL 238

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            + K G   ++ IK   +++   +  + +    + L   L+N +N V   E+++L +  N 
Sbjct: 239  YAKHGPEHKAVIKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNV 298

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L 
Sbjct: 299  AKMPRKDFIRSWENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKVNSLT 358

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L D+++INR M+ GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 359  LADIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 418

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AV KFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ 
Sbjct: 419  AVCKFEHRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQF 478

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D 
Sbjct: 479  GREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDT 538

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
              N ++   V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 539  TTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 598

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR  +L+ FL+
Sbjct: 599  LRKLRHPSRSEQLRSFLD 616



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 306/605 (50%), Positives = 411/605 (67%), Gaps = 35/605 (5%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 101
            K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 12  IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 71

Query: 102 ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDG---LIDKNFSSNNRVIKG 213
           EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G   LI+++ S  + V   
Sbjct: 132 EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDLIEEDNSVTSSVDVT 190

Query: 214 NKN-------------NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
           +++             N+E+  +I    A++++            +  ++S  + K +K 
Sbjct: 191 DESIVEVDEEDDDSVGNDEDAPMIGPDPAEVAS------------RIESLSTEYAKFKKL 238

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           + K G   ++ IK   +++   +  + +    + L   L+N +N V   E+++L +  N 
Sbjct: 239 YAKHGPEHKAVIKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNV 298

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L 
Sbjct: 299 AKMPRKDFIRSWENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKVNSLT 358

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L D+++INR M+ GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 359 LADIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 418

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AV KFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ 
Sbjct: 419 AVCKFEHRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQF 478

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D 
Sbjct: 479 GREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDT 538

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
             N ++   V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 539 TTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 598

Query: 621 LRKLR 625
           LRKLR
Sbjct: 599 LRKLR 603


>gi|152999721|ref|YP_001365402.1| RNA polymerase sigma-70 subunit RpoD [Shewanella baltica OS185]
 gi|160874340|ref|YP_001553656.1| RNA polymerase sigma-70 subunit RpoD [Shewanella baltica OS195]
 gi|151364339|gb|ABS07339.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS185]
 gi|160859862|gb|ABX48396.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS195]
          Length = 627

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 417/612 (68%), Gaps = 24/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 24   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 83

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 84   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 144  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 203

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
             +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 204  LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 263

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 264  FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 323

Query: 1126 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 324  ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 374

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 375  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 434

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 435  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 494

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 495  EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 554

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 555  KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 614

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 615  PSRSEILKSFLD 626



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 408/599 (68%), Gaps = 24/599 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 24  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 83

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 84  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 144 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 203

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
            +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 204 LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 263

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 264 FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 323

Query: 336 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 324 ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 374

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 375 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 434

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 435 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 494

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 495 EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 554

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|28198503|ref|NP_778817.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa Temecula1]
 gi|182681181|ref|YP_001829341.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M23]
 gi|417559201|ref|ZP_12210153.1| DNA-directed RNA polymerase sigma subunit sigma70/sigma32 [Xylella
            fastidiosa EB92.1]
 gi|28056587|gb|AAO28466.1| RNA polymerase sigma-70 factor [Xylella fastidiosa Temecula1]
 gi|182631291|gb|ACB92067.1| RNA polymerase, sigma 70 subunit, RpoD [Xylella fastidiosa M23]
 gi|338178180|gb|EGO81173.1| DNA-directed RNA polymerase sigma subunit sigma70/sigma32 [Xylella
            fastidiosa EB92.1]
          Length = 623

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 313/618 (50%), Positives = 421/618 (68%), Gaps = 35/618 (5%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 891
             K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17   IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 892  ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77   EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDG---LIDKNFSSNNRVIKG 1003
            EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G   LI+++ S  + V   
Sbjct: 137  EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDLIEEDNSVTSSVDVT 195

Query: 1004 NKN-------------NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
            +++             N+E+  +I    A++++            +  ++S  + K +K 
Sbjct: 196  DESIVEVDEEDDDSVGNDEDAPMIGPDPAEVAS------------RIESLSTEYAKFKKL 243

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
            + K G   ++ IK   +++   +  + +    + L   L+N +N V   E+++L +  N 
Sbjct: 244  YAKHGPEHKAVIKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNV 303

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MPR  FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L 
Sbjct: 304  AKMPRKDFIRSWENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKVNSLT 363

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            L D+++INR M+ GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 364  LADIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 423

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AV KFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ 
Sbjct: 424  AVCKFEHRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQF 483

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D 
Sbjct: 484  GREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDT 543

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
              N ++   V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 544  TTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 603

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR  +L+ FL+
Sbjct: 604  LRKLRHPSRSEQLRSFLD 621



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 306/605 (50%), Positives = 411/605 (67%), Gaps = 35/605 (5%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 101
            K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17  IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 102 ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77  EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDG---LIDKNFSSNNRVIKG 213
           EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G   LI+++ S  + V   
Sbjct: 137 EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDLIEEDNSVTSSVDVT 195

Query: 214 NKN-------------NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
           +++             N+E+  +I    A++++            +  ++S  + K +K 
Sbjct: 196 DESIVEVDEEDDDSVGNDEDAPMIGPDPAEVAS------------RIESLSTEYAKFKKL 243

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
           + K G   ++ IK   +++   +  + +    + L   L+N +N V   E+++L +  N 
Sbjct: 244 YAKHGPEHKAVIKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNV 303

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MPR  FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L 
Sbjct: 304 AKMPRKDFIRSWENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKVNSLT 363

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           L D+++INR M+ GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 364 LADIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 423

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AV KFE+RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ 
Sbjct: 424 AVCKFEHRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQF 483

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D 
Sbjct: 484 GREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDT 543

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
             N ++   V+++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 544 TTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 603

Query: 621 LRKLR 625
           LRKLR
Sbjct: 604 LRKLR 608


>gi|315634867|ref|ZP_07890149.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            segnis ATCC 33393]
 gi|315476419|gb|EFU67169.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            segnis ATCC 33393]
          Length = 621

 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 304/621 (48%), Positives = 416/621 (66%), Gaps = 22/621 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   + ++
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVESGGVRLADLITGFVDPNVLSESETAELDE 181

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFDKM 1047
             ++EE    E+ +A    ++ E  +                       KF+ +     K 
Sbjct: 182  FHSEEGE--ENVAAAEIDDESEDEEDSEESASDDSDSDNSIDPEVAREKFTALRQQHQKT 239

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
             +   K G   +        +S+     R   K  + L  + R+ + +V   E+ I  +V
Sbjct: 240  LEIIAKHGRTGKKAKDEIQALSDIFTQFRLVPKQFDTLVLSTRDMMKRVRHQERLIQRLV 299

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V+   MP+  F K F  +E +  W+         ++  L +    +++    L+ ++ D 
Sbjct: 300  VDNAKMPKSSFQKSFIGHETSDVWLVKALAAGKSWSEKLAQYEDELRQAIAHLVQIEQDT 359

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 360  NLTIGQIREIGERISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 419

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 420  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 479

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P
Sbjct: 480  QEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELP 539

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 540  LDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 599

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 600  AKALRKLRHPSRSETLRSFLD 620



 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/608 (48%), Positives = 407/608 (66%), Gaps = 22/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   + ++
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVESGGVRLADLITGFVDPNVLSESETAELDE 181

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFDKM 257
            ++EE    E+ +A    ++ E  +                       KF+ +     K 
Sbjct: 182 FHSEEGE--ENVAAAEIDDESEDEEDSEESASDDSDSDNSIDPEVAREKFTALRQQHQKT 239

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
            +   K G   +        +S+     R   K  + L  + R+ + +V   E+ I  +V
Sbjct: 240 LEIIAKHGRTGKKAKDEIQALSDIFTQFRLVPKQFDTLVLSTRDMMKRVRHQERLIQRLV 299

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V+   MP+  F K F  +E +  W+         ++  L +    +++    L+ ++ D 
Sbjct: 300 VDNAKMPKSSFQKSFIGHETSDVWLVKALAAGKSWSEKLAQYEDELRQAIAHLVQIEQDT 359

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 360 NLTIGQIREIGERISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 419

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 420 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 479

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P
Sbjct: 480 QEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELP 539

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 540 LDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 599

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 600 AKALRKLR 607


>gi|30064415|ref|NP_838586.1| RNA polymerase sigma factor RpoD [Shigella flexneri 2a str. 2457T]
 gi|30042672|gb|AAP18396.1| sigmaD(70) factor of RNA polymerase [Shigella flexneri 2a str. 2457T]
          Length = 608

 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 408/601 (67%), Gaps = 8/601 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 R 1419
            R
Sbjct: 603  R 603



 Score =  565 bits (1455), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 294/597 (49%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|406979799|gb|EKE01510.1| hypothetical protein ACD_21C00111G0002 [uncultured bacterium]
          Length = 739

 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/658 (47%), Positives = 416/658 (63%), Gaps = 54/658 (8%)

Query: 824  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISVSEH 882
            E +   + + K LI  GK++GYLTF+E+ND LP +I+D + IE II      M I + E 
Sbjct: 83   EALTKQKTELKNLITKGKDQGYLTFTEVNDNLPPEIVDPDQIEDIIGMLNEDMGIPIYED 142

Query: 883  VLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
              DTE  +L++ T     EE     ++  D + GRT DP++MYMREMG+VELLTR GEI 
Sbjct: 143  TPDTEATLLNDNTPIITEEEQATPVVAAED-ETGRTSDPVRMYMREMGTVELLTRSGEIA 201

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG-------------- 988
            IAKRIEEG K ++ A++  P  I  IL    K    + ++ EI+ G              
Sbjct: 202  IAKRIEEGSKHVLSALAQYPGIIDSILAEYAKTETTDKRLQEIISGFYDIEEWHTPPTDA 261

Query: 989  ----------------LIDKNFSSNNRV-------IKGNKNNNEEKILIESSSADLSTEQ 1025
                            + D N  +   +       IK +++ +E+    E S+ D + +Q
Sbjct: 262  QKIVTLETVTESSITSITDDNIETTEEITLKTTTRIKKDEDEDEDATNEEESTDDKALDQ 321

Query: 1026 LEKLKYE---------------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 1070
             E    E               +  +F+ +     +  KA  K G + +   K H  + +
Sbjct: 322  DESESTEDDELDLFESGPDPVVAKERFTELYELNRQYTKALAKNGESHKKTTKLHQQLID 381

Query: 1071 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 1130
                 + T K   K    L   + ++   E  I+E+ + K  + R  FI  FP +E +L 
Sbjct: 382  AFTKFKLTPKEFHKQTTKLSKILERIRANEHLIMELCIKKSKVARKAFINSFPHHETDLK 441

Query: 1131 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 1190
            WVD   K   +    L  N   I   Q+KL+ ++ ++ L + ++++I+R++ AG+ K RK
Sbjct: 442  WVDKFAKANKNQAAALLHNAKEIHRAQKKLLAIEKEVNLSIAEIKNISRQVTAGDTKTRK 501

Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
            AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 502  AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 561

Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
            IRQAITRSIADQARTIRIPVHMIETINK++RISRQI+QETG EP P  ++++M+M E+K+
Sbjct: 562  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQIIQETGVEPSPEELSVRMQMHEDKV 621

Query: 1311 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 1370
            RK++KIAKEP+SME+P+GDDEDSHLGDFIED N L+P+D+A +  +R    D+L+SLTPR
Sbjct: 622  RKVLKIAKEPISMETPIGDDEDSHLGDFIEDANTLSPTDSATHGGLREATNDVLSSLTPR 681

Query: 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            E+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KL+ F++
Sbjct: 682  EAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEKLQSFVD 739



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/645 (47%), Positives = 406/645 (62%), Gaps = 54/645 (8%)

Query: 34  EEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISVSEH 92
           E +   + + K LI  GK++GYLTF+E+ND LP +I+D + IE II      M I + E 
Sbjct: 83  EALTKQKTELKNLITKGKDQGYLTFTEVNDNLPPEIVDPDQIEDIIGMLNEDMGIPIYED 142

Query: 93  VLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
             DTE  +L++ T     EE     ++  D + GRT DP++MYMREMG+VELLTR GEI 
Sbjct: 143 TPDTEATLLNDNTPIITEEEQATPVVAAED-ETGRTSDPVRMYMREMGTVELLTRSGEIA 201

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG-------------- 198
           IAKRIEEG K ++ A++  P  I  IL    K    + ++ EI+ G              
Sbjct: 202 IAKRIEEGSKHVLSALAQYPGIIDSILAEYAKTETTDKRLQEIISGFYDIEEWHTPPTDA 261

Query: 199 ----------------LIDKNFSSNNRV-------IKGNKNNNEEKILIESSSADLSTEQ 235
                           + D N  +   +       IK +++ +E+    E S+ D + +Q
Sbjct: 262 QKIVTLETVTESSITSITDDNIETTEEITLKTTTRIKKDEDEDEDATNEEESTDDKALDQ 321

Query: 236 LEKLKYE---------------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 280
            E    E               +  +F+ +     +  KA  K G + +   K H  + +
Sbjct: 322 DESESTEDDELDLFESGPDPVVAKERFTELYELNRQYTKALAKNGESHKKTTKLHQQLID 381

Query: 281 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 340
                + T K   K    L   + ++   E  I+E+ + K  + R  FI  FP +E +L 
Sbjct: 382 AFTKFKLTPKEFHKQTTKLSKILERIRANEHLIMELCIKKSKVARKAFINSFPHHETDLK 441

Query: 341 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 400
           WVD   K   +    L  N   I   Q+KL+ ++ ++ L + ++++I+R++ AG+ K RK
Sbjct: 442 WVDKFAKANKNQAAALLHNAKEIHRAQKKLLAIEKEVNLSIAEIKNISRQVTAGDTKTRK 501

Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
           AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 502 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 561

Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
           IRQAITRSIADQARTIRIPVHMIETINK++RISRQI+QETG EP P  ++++M+M E+K+
Sbjct: 562 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQIIQETGVEPSPEELSVRMQMHEDKV 621

Query: 521 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 580
           RK++KIAKEP+SME+P+GDDEDSHLGDFIED N L+P+D+A +  +R    D+L+SLTPR
Sbjct: 622 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDANTLSPTDSATHGGLREATNDVLSSLTPR 681

Query: 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           E+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 682 EAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 726


>gi|15837951|ref|NP_298639.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa 9a5c]
 gi|20140311|sp|Q9PDM9.1|RPOD_XYLFA RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|9106350|gb|AAF84159.1|AE003967_3 RNA polymerase sigma-70 factor [Xylella fastidiosa 9a5c]
          Length = 618

 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 411/607 (67%), Gaps = 13/607 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 891
             K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 12   IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 71

Query: 892  ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            EEGL ++  A+   P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 132  EEGLSEVQAALGVFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEEDNSVTSSVDV 189

Query: 1007 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 190  TDESIVEVDEEDDDSVGNDEDAPTIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 250  IKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRS 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 310  WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMM 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
            + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 370  VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 490  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 610  QLRSFLD 616



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/594 (51%), Positives = 401/594 (67%), Gaps = 13/594 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 101
            K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 12  IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 71

Query: 102 ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           EEGL ++  A+   P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 132 EEGLSEVQAALGVFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEEDNSVTSSVDV 189

Query: 217 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 190 TDESIVEVDEEDDDSVGNDEDAPTIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 250 IKVREDVAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRS 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 310 WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQASIDLEKANSLTLADIKEINRMM 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
           + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 370 VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 490 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|126173383|ref|YP_001049532.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125996588|gb|ABN60663.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS155]
          Length = 627

 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 310/612 (50%), Positives = 417/612 (68%), Gaps = 24/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 24   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 83

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 84   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 144  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 203

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
             +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 204  LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 263

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 264  FEIGEIFKEFRLVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 323

Query: 1126 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 324  ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 374

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 375  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 434

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 435  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 494

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 495  EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 554

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 555  KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 614

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 615  PSRSEILKSFLD 626



 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 408/599 (68%), Gaps = 24/599 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 24  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 83

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 84  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 143

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 144 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 203

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
            +   +    D + ++ E  K     E+  +F  +   ++   K  E +G      +KA 
Sbjct: 204 LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIEAKGREHPESVKAL 263

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K+F  N
Sbjct: 264 FEIGEIFKEFRLVPKQFDRLVKSIRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKLFTGN 323

Query: 336 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 324 ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 374

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 375 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 434

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 435 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 494

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 495 EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 554

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|222157794|ref|YP_002557933.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
 gi|222034799|emb|CAP77541.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
          Length = 613

 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 412/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIA QARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIAVQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 403/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDTADDDNSIDPELAREKFAELRAQYIVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIA QARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIAVQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|254429850|ref|ZP_05043557.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
 gi|196196019|gb|EDX90978.1| Sigma-70, non-essential region family [Alcanivorax sp. DG881]
          Length = 633

 Score =  575 bits (1481), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 305/624 (48%), Positives = 421/624 (67%), Gaps = 39/624 (6%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 894
            I LGKE+GYLT++E+ND LP+ I D + +E II+    M I+V E   D + L +  S  
Sbjct: 16   IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            ++D+   E   A L++V+++ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76   STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIV--------DGLIDKNFSSNNRVIKGNKN 1006
            +HA++  P  +  ++    ++   E K+ +I+        DG    N + +    +  K 
Sbjct: 136  LHALAFWPGAVDMVIDEYARVENEERKLTDIIAGYLDPNDDGAAATNVNRDPAFAEKAKK 195

Query: 1007 NNEEKILIESSSADLSTEQ-----------------LEKLKYESLIKFSNISFHFDKMRK 1049
              EEK   +  + +  T+                  L   ++E+L K        +K  +
Sbjct: 196  AAEEKAKAKEKAKEEGTDDKDSDDDEEEDEGGLDPVLAAERFETLKKL------HEKAER 249

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            + ++ G +  S  KA   ++      +   +  + +    R+ ++ V + E+QI+   + 
Sbjct: 250  SLKRNGRDHASSAKALEALAEHFTLFKLVPRIFDGMLVGARDNLDLVRKFERQIMSATIR 309

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQT 1165
            + GM R  FIKVFP NE N++W+D + K +      +   + ++KE     Q+K+  ++ 
Sbjct: 310  RGGMDRKDFIKVFPGNETNMDWIDGQLKTKK--GKAIADKLGAVKEDVQRAQRKIGTIED 367

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
             I LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 368  IIGLPVGDIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 427

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ
Sbjct: 428  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQ 487

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM 
Sbjct: 488  MLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNME 547

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
            +P D+A +  +    +D+L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 548  SPVDSATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 607

Query: 1406 IEAKALRKLRHPSRYYKLKIFLEG 1429
            IEAKALRKLRHPSR   L+ FL+G
Sbjct: 608  IEAKALRKLRHPSRSEHLRSFLDG 631



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 297/610 (48%), Positives = 411/610 (67%), Gaps = 39/610 (6%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SNI 104
           I LGKE+GYLT++E+ND LP+ I D + +E II+    M I+V E   D + L +  S  
Sbjct: 16  IALGKEQGYLTYAEVNDHLPDSITDTDQVEDIIQMINDMGITVVEKAADADQLTIDESAD 75

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           ++D+   E   A L++V+++ GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG +++
Sbjct: 76  STDEVAAEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGTREV 135

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIV--------DGLIDKNFSSNNRVIKGNKN 216
           +HA++  P  +  ++    ++   E K+ +I+        DG    N + +    +  K 
Sbjct: 136 LHALAFWPGAVDMVIDEYARVENEERKLTDIIAGYLDPNDDGAAATNVNRDPAFAEKAKK 195

Query: 217 NNEEKILIESSSADLSTEQ-----------------LEKLKYESLIKFSNISFHFDKMRK 259
             EEK   +  + +  T+                  L   ++E+L K        +K  +
Sbjct: 196 AAEEKAKAKEKAKEEGTDDKDSDDDEEEDEGGLDPVLAAERFETLKKL------HEKAER 249

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
           + ++ G +  S  KA   ++      +   +  + +    R+ ++ V + E+QI+   + 
Sbjct: 250 SLKRNGRDHASSAKALEALAEHFTLFKLVPRIFDGMLVGARDNLDLVRKFERQIMSATIR 309

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQT 375
           + GM R  FIKVFP NE N++W+D + K +      +   + ++KE     Q+K+  ++ 
Sbjct: 310 RGGMDRKDFIKVFPGNETNMDWIDGQLKTKK--GKAIADKLGAVKEDVQRAQRKIGTIED 367

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
            I LP+ D+++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 368 IIGLPVGDIKEINRRISIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 427

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+ RQ
Sbjct: 428 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVQRQ 487

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G EP P  + +++EMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED NM 
Sbjct: 488 MLQEMGREPTPEELGVRLEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDGNME 547

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
           +P D+A +  +    +D+L +LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 548 SPVDSATSLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 607

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 608 IEAKALRKLR 617


>gi|91794185|ref|YP_563836.1| RNA polymerase sigma factor RpoD-like protein [Shewanella
            denitrificans OS217]
 gi|91716187|gb|ABE56113.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella denitrificans
            OS217]
          Length = 617

 Score =  575 bits (1481), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/613 (50%), Positives = 413/613 (67%), Gaps = 19/613 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +
Sbjct: 9    QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 890  MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            M+S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 69   MMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 128

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            G+  +  ++S  P  I  IL   D+   +E+++ +I+ G I+ +    + V     N   
Sbjct: 129  GINTVQSSVSEYPQAIAMILEQFDQYEADELRLTDIIAGFINPD---EDDVAPTATNIGS 185

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSN-------ISFHFDKMRKAFEK-------EG 1055
            E  L E+   D   +  +    +   +  N           F ++R+ +EK       +G
Sbjct: 186  E--LSEAQQNDDDNDDDDDDSDDEEEEEGNKGPDPEQAKEKFTELREVYEKGLAVIAEKG 243

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +    I A   I       R   K  ++L  ++R  +++V   E+ IL++ V +  MP+
Sbjct: 244  RDHPEAIGALFVIGELFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLILKLCVEQAKMPK 303

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             +F+K F  NE NL+W + E      Y   L      +     KL  ++ +  L ++ ++
Sbjct: 304  KNFVKAFTSNETNLDWFNKEMNSNKPYADALKAVAHDVNRCSSKLTAIELETDLTISSIK 363

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 364  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 423

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 424  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 483

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 484  PEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 543

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544  LKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   LK FL+
Sbjct: 604  HPSRSEILKSFLD 616



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 304/600 (50%), Positives = 404/600 (67%), Gaps = 19/600 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 100 MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           M+S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 128

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           G+  +  ++S  P  I  IL   D+   +E+++ +I+ G I+ +    + V     N   
Sbjct: 129 GINTVQSSVSEYPQAIAMILEQFDQYEADELRLTDIIAGFINPD---EDDVAPTATNIGS 185

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSN-------ISFHFDKMRKAFEK-------EG 265
           E  L E+   D   +  +    +   +  N           F ++R+ +EK       +G
Sbjct: 186 E--LSEAQQNDDDNDDDDDDSDDEEEEEGNKGPDPEQAKEKFTELREVYEKGLAVIAEKG 243

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +    I A   I       R   K  ++L  ++R  +++V   E+ IL++ V +  MP+
Sbjct: 244 RDHPEAIGALFVIGELFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLILKLCVEQAKMPK 303

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            +F+K F  NE NL+W + E      Y   L      +     KL  ++ +  L ++ ++
Sbjct: 304 KNFVKAFTSNETNLDWFNKEMNSNKPYADALKAVAHDVNRCSSKLTAIELETDLTISSIK 363

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 364 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 423

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 424 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPS 483

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S
Sbjct: 484 PEELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSES 543

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 LKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|392308108|ref|ZP_10270642.1| RNA polymerase sigma factor [Pseudoalteromonas citrea NCIMB 1889]
          Length = 612

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 316/612 (51%), Positives = 409/612 (66%), Gaps = 21/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V+E+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVAENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIKIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +IV G  D +              +   
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIVSGFFDPDAEETQ--------ISATH 179

Query: 1012 ILIESSSADLSTEQLEKLKY-------------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
            I  E S  DL+ E  E                 E+   F  +   +   RK FE +G + 
Sbjct: 180  IGSELSDKDLADEDNESDDDDDEDEVDTGPDPEEAREHFEKLRELYTAARKVFESKGRSH 239

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                 A   I +     +   K  +++ + +R  +++V   E+ +++  V    +P+  F
Sbjct: 240  PDAQIAIQEIGDLFRTFKLVPKQFDRMVNNMREMMDRVRVQERIVMKQAVQIAKVPKKTF 299

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +K F  NE ++ WVD E      Y+  L    P I+    KL  ++    L +  ++DIN
Sbjct: 300  VKHFANNETDMAWVDAEIAAGEKYSAKLAEVKPEIERCINKLSVIEESTGLSIERIKDIN 359

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 360  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 419

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 420  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEE 479

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R 
Sbjct: 480  LAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRG 539

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 540  ATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 599

Query: 1419 RYYKLKIFLEGK 1430
            R   LK FL+ K
Sbjct: 600  RSDLLKSFLDVK 611



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 310/605 (51%), Positives = 402/605 (66%), Gaps = 22/605 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V+E+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIKVAENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIKIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +IV G  D +              +   
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKFEAEEMRLSDIVSGFFDPDAEETQ--------ISATH 179

Query: 222 ILIESSSADLSTEQLEKLKY-------------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
           I  E S  DL+ E  E                 E+   F  +   +   RK FE +G + 
Sbjct: 180 IGSELSDKDLADEDNESDDDDDEDEVDTGPDPEEAREHFEKLRELYTAARKVFESKGRSH 239

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
                A   I +     +   K  +++ + +R  +++V   E+ +++  V    +P+  F
Sbjct: 240 PDAQIAIQEIGDLFRTFKLVPKQFDRMVNNMREMMDRVRVQERIVMKQAVQIAKVPKKTF 299

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           +K F  NE ++ WVD E      Y+  L    P I+    KL  ++    L +  ++DIN
Sbjct: 300 VKHFANNETDMAWVDAEIAAGEKYSAKLAEVKPEIERCINKLSVIEESTGLSIERIKDIN 359

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 360 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 419

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 420 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEE 479

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R 
Sbjct: 480 LAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRG 539

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PL 627
              ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P 
Sbjct: 540 ATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 599

Query: 628 AHDWL 632
             D L
Sbjct: 600 RSDLL 604


>gi|113971243|ref|YP_735036.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
 gi|113885927|gb|ABI39979.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-4]
          Length = 619

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/608 (50%), Positives = 409/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 1008
              +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131  NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 1009 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +     +    +      +            E+  +F  +   ++   K  E +G     
Sbjct: 191  DLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYENALKIIEAKGREHPE 250

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             IKA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251  SIKALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311  FFTGNETNLDWFDAEKNSNKPYAEGLKMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 551  HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 610

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 611  EILKSFLD 618



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 400/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 218
             +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 219 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +     +    +      +            E+  +F  +   ++   K  E +G     
Sbjct: 191 DLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYENALKIIEAKGREHPE 250

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            IKA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251 SIKALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311 FFTGNETNLDWFDAEKNSNKPYAEGLKMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|407715366|ref|YP_006836646.1| RNA polymerase sigma factor [Cycloclasticus sp. P1]
 gi|407255702|gb|AFT66143.1| RNA polymerase sigma factor [Cycloclasticus sp. P1]
          Length = 600

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 303/603 (50%), Positives = 414/603 (68%), Gaps = 23/603 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            K K LI  G E+GYLT++E+ND LP+D+ + E IE II     M ISVSE   +++T+  
Sbjct: 12   KIKALISKGHEQGYLTYAEVNDHLPQDV-EPERIEEIITMISDMGISVSEEAPESDTV-- 68

Query: 892  SNITSDDDVEEATEAALSTV-----DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            S+ T    V+E+  A ++ V     D + GRT DP++MYMREMG+V LLTR GE++IAKR
Sbjct: 69   SDGTVAQTVDESAAAEVAAVALATVDKELGRTTDPVRMYMREMGTVGLLTRQGELDIAKR 128

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEG  +M+ AI   P  +       +KI  +E+++ + +   +D         ++ + +
Sbjct: 129  IEEGQNEMLAAIVRYPAVVDRFFDVFEKIKSDELRLADYIPDFVD---------LEDDYD 179

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESL-IKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
              +      +++ D S  ++  L  E + ++ + I+  + +  K  +KEGY SE   K  
Sbjct: 180  YTQP-----AAAKDESAPEIPALTIEDVEVRINEIAAKYKECTKVIKKEGYASEKTQKEF 234

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
            + ++   + ++FT +    L + ++  +  V   EK I++I V +  MPR  FI  F +N
Sbjct: 235  DELALLFMALKFTPRFFTLLSNEMKQCVELVRAQEKTIIDICVKQAKMPRKLFIAGFVKN 294

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E ++ W++   K    +  ++  N   IK+ Q +L N++++  L   +++DINR++  GE
Sbjct: 295  ESDITWLEEHLKTDEPFVAVIKENFHEIKKAQVRLANVESESSLVTTEIKDINRRLSIGE 354

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             K R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 355  AKMRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 414

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +AI+MEM
Sbjct: 415  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEKGREALPEELAIEMEM 474

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+K+RK++KIAKEP+SM +P+GDDEDS LGDFIED N ++P D+A   S+R   +D+L 
Sbjct: 475  PEDKVRKVLKIAKEPISMGTPIGDDEDSSLGDFIEDANAVSPVDSATIESLRESTQDVLA 534

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
             LT RE+KV+RMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ 
Sbjct: 535  GLTAREAKVIRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRTEHLRS 594

Query: 1426 FLE 1428
            F++
Sbjct: 595  FID 597



 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/590 (50%), Positives = 405/590 (68%), Gaps = 23/590 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           K K LI  G E+GYLT++E+ND LP+D+ + E IE II     M ISVSE   +++T+  
Sbjct: 12  KIKALISKGHEQGYLTYAEVNDHLPQDV-EPERIEEIITMISDMGISVSEEAPESDTV-- 68

Query: 102 SNITSDDDVEEATEAALSTV-----DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           S+ T    V+E+  A ++ V     D + GRT DP++MYMREMG+V LLTR GE++IAKR
Sbjct: 69  SDGTVAQTVDESAAAEVAAVALATVDKELGRTTDPVRMYMREMGTVGLLTRQGELDIAKR 128

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEG  +M+ AI   P  +       +KI  +E+++ + +   +D         ++ + +
Sbjct: 129 IEEGQNEMLAAIVRYPAVVDRFFDVFEKIKSDELRLADYIPDFVD---------LEDDYD 179

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESL-IKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
             +      +++ D S  ++  L  E + ++ + I+  + +  K  +KEGY SE   K  
Sbjct: 180 YTQP-----AAAKDESAPEIPALTIEDVEVRINEIAAKYKECTKVIKKEGYASEKTQKEF 234

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
           + ++   + ++FT +    L + ++  +  V   EK I++I V +  MPR  FI  F +N
Sbjct: 235 DELALLFMALKFTPRFFTLLSNEMKQCVELVRAQEKTIIDICVKQAKMPRKLFIAGFVKN 294

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E ++ W++   K    +  ++  N   IK+ Q +L N++++  L   +++DINR++  GE
Sbjct: 295 ESDITWLEEHLKTDEPFVAVIKENFHEIKKAQVRLANVESESSLVTTEIKDINRRLSIGE 354

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            K R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 355 AKMRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 414

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +AI+MEM
Sbjct: 415 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEKGREALPEELAIEMEM 474

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+K+RK++KIAKEP+SM +P+GDDEDS LGDFIED N ++P D+A   S+R   +D+L 
Sbjct: 475 PEDKVRKVLKIAKEPISMGTPIGDDEDSSLGDFIEDANAVSPVDSATIESLRESTQDVLA 534

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KV+RMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 535 GLTAREAKVIRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|71274854|ref|ZP_00651142.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
            region 4:Sigma-70, non-essential region:Sigma-70 region
            1.2 [Xylella fastidiosa Dixon]
 gi|170729898|ref|YP_001775331.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa M12]
 gi|71164586|gb|EAO14300.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
            region 4:Sigma-70, non-essential region:Sigma-70 region
            1.2 [Xylella fastidiosa Dixon]
 gi|71728114|gb|EAO30313.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
            region 4:Sigma-70, non-essential region:Sigma-70 region
            1.2 [Xylella fastidiosa Ann-1]
 gi|167964691|gb|ACA11701.1| RNA polymerase sigma-70 factor [Xylella fastidiosa M12]
          Length = 623

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/607 (51%), Positives = 412/607 (67%), Gaps = 13/607 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 891
             K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17   IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 892  ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77   EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 137  EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEDDNSVTSSVDV 194

Query: 1007 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 195  TDESIVEVDEEDDDSVGNDEDAPMIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 254

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 255  IKVREDMAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRS 314

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 315  WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQSSIDLEKVNSLTLADIKEINRMM 374

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
            + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 375  VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 434

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 435  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 494

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 495  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 554

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 555  EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 614

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 615  QLRSFLD 621



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/594 (51%), Positives = 402/594 (67%), Gaps = 13/594 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML- 101
            K LI  G E+GYLT++E+ND LPED++D + IE II     M I V E   D ETL+L 
Sbjct: 17  IKQLISKGLEQGYLTYAEVNDHLPEDLVDPDQIEDIIGMINGMGIEVHEVAPDAETLLLN 76

Query: 102 ----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77  EGNTGNREVDDTAAEEAAAALSALDTEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISK-NEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           EEGL ++  A+ + P +  E+L++  ++ K  + ++ E+V G  D     +N V      
Sbjct: 137 EEGLSEVQAALGAFPLST-ELLLSEYELHKEGKRRLTEVVVGFNDL-IEDDNSVTSSVDV 194

Query: 217 NNEEKILIE-----SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            +E  + ++     S   D     +     E   +  ++S  + K +K + K G   ++ 
Sbjct: 195 TDESIVEVDEEDDDSVGNDEDAPMIGPDPAEVASRIESLSTEYAKFKKLYAKHGPEHKAV 254

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           IK   +++   +  + +    + L   L+N +N V   E+++L +  N   MPR  FI+ 
Sbjct: 255 IKVREDMAAIFVTFKLSLPLTDLLVQQLQNMVNSVKDHERKVLHLATNVAKMPRKDFIRS 314

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N+ NL WV++  K +  ++  L      I   QQ  I+L+    L L D+++INR M
Sbjct: 315 WENNQTNLEWVEDAIKRKQKWSSALRDIKDQITAEQQSSIDLEKVNSLTLADIKEINRMM 374

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
           + GE KA KAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV KFE+RRG+
Sbjct: 375 VYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGF 434

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 435 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEELAK 494

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++   V+
Sbjct: 495 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDPNVESPVDTTTNVNLSETVR 554

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 555 EVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608


>gi|416051968|ref|ZP_11577943.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans serotype e str. SC1083]
 gi|347992579|gb|EGY33971.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans serotype e str. SC1083]
          Length = 616

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/617 (49%), Positives = 413/617 (66%), Gaps = 19/617 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNMLSESETEELAE 181

Query: 1006 NNNEEK--------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
            + N E+                + S  +D       ++  E   KF+ +     K  ++ 
Sbjct: 182  DFNSEEDGGIDNEHEEEEDNEEVSSDDSDSDNSIDPEIARE---KFTALKQQHQKTLESI 238

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             K G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV   
Sbjct: 239  AKHGRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRSQERFIQRIVVENA 298

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  F K F  +E    W+         ++  L +    +++     + ++ D  L +
Sbjct: 299  KMPKSGFQKSFIGHETTDTWLVKALSAGKSWSEKLAQYENQLRQAITNFVQIEQDTHLTI 358

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359  PQIREIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A
Sbjct: 479  REASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSA 538

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S+++   +IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539  TVQSLKAATHEILEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 599  RKLRHPSRSETLRSFLD 615



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/604 (49%), Positives = 404/604 (66%), Gaps = 19/604 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  S +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNMLSESETEELAE 181

Query: 216 NNNEEK--------------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
           + N E+                + S  +D       ++  E   KF+ +     K  ++ 
Sbjct: 182 DFNSEEDGGIDNEHEEEEDNEEVSSDDSDSDNSIDPEIARE---KFTALKQQHQKTLESI 238

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            K G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV   
Sbjct: 239 AKHGRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRSQERFIQRIVVENA 298

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  F K F  +E    W+         ++  L +    +++     + ++ D  L +
Sbjct: 299 KMPKSGFQKSFIGHETTDTWLVKALSAGKSWSEKLAQYENQLRQAITNFVQIEQDTHLTI 358

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 359 PQIREIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 418

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 419 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 478

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A
Sbjct: 479 REASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSA 538

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S+++   +IL  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 539 TVQSLKAATHEILEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 622 RKLR 625
           RKLR
Sbjct: 599 RKLR 602


>gi|348030229|ref|YP_004872915.1| RNA polymerase sigma factor [Glaciecola nitratireducens FR1064]
 gi|347947572|gb|AEP30922.1| RNA polymerase sigma factor [Glaciecola nitratireducens FR1064]
          Length = 608

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 307/607 (50%), Positives = 422/607 (69%), Gaps = 4/607 (0%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D
Sbjct: 1    MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVSESAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             + L++ + ++D+DV EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61   ADELLMQDSSADEDVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 1002
            RIE+G+  +  +++  P  I  +L   D     EI+I +I+ G +D N    +     I 
Sbjct: 121  RIEDGINQVQCSVAEYPEAITYLLDQWDLFEAEEIRISDIIIGFVDPNEQDVAPTATHIG 180

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
               +  E     + +  +   E+   +  E +  KF+ +   ++K+    E +G + ++ 
Sbjct: 181  SELSQEELDDEDDDADDEDEEEEDTGVDPELAREKFTALRNQYNKVMSVIEVKGRSHKAS 240

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             K  + +S      R   K  +++   +R  +++V   E+ +++  V    MP+  FIK 
Sbjct: 241  RKEIHELSEVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLVMKYCVMNAKMPKKDFIKA 300

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE +++W+    + +  Y   L      I+    K+  ++ +  L + D++DINR+M
Sbjct: 301  FAGNETSIDWLYKALEGKAPYVEKLLEFKEEIERSVSKMNAVEAETGLIIPDIKDINRRM 360

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 361  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 420

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ 
Sbjct: 421  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSE 480

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+++  +
Sbjct: 481  RMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKNATQ 540

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 541  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 600

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 601  QLRSFLD 607



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 300/594 (50%), Positives = 412/594 (69%), Gaps = 4/594 (0%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I VSE   D
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVSESAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            + L++ + ++D+DV EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61  ADELLMQDSSADEDVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 212
           RIE+G+  +  +++  P  I  +L   D     EI+I +I+ G +D N    +     I 
Sbjct: 121 RIEDGINQVQCSVAEYPEAITYLLDQWDLFEAEEIRISDIIIGFVDPNEQDVAPTATHIG 180

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
              +  E     + +  +   E+   +  E +  KF+ +   ++K+    E +G + ++ 
Sbjct: 181 SELSQEELDDEDDDADDEDEEEEDTGVDPELAREKFTALRNQYNKVMSVIEVKGRSHKAS 240

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            K  + +S      R   K  +++   +R  +++V   E+ +++  V    MP+  FIK 
Sbjct: 241 RKEIHELSEVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLVMKYCVMNAKMPKKDFIKA 300

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE +++W+    + +  Y   L      I+    K+  ++ +  L + D++DINR+M
Sbjct: 301 FAGNETSIDWLYKALEGKAPYVEKLLEFKEEIERSVSKMNAVEAETGLIIPDIKDINRRM 360

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 361 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 420

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ 
Sbjct: 421 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSE 480

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+++  +
Sbjct: 481 RMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKNATQ 540

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|147674012|ref|YP_001216017.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|227116893|ref|YP_002818789.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|146315895|gb|ABQ20434.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
 gi|227012343|gb|ACP08553.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O395]
          Length = 621

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 318/625 (50%), Positives = 419/625 (67%), Gaps = 30/625 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 1043
                   I  E S ADL+ E    ++ E                        KF+ +   
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGK 235

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   E+ +
Sbjct: 236  FQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLV 295

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
            ++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QKL  +
Sbjct: 296  MKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMI 355

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  L +  ++DI+ +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 356  EQETSLSVERIKDISHRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 415

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 416  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 475

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 476  RQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 535

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 536  LELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 595

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RQIEAKALRKLRHPSRSEVLRSFLD 620



 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 311/612 (50%), Positives = 410/612 (66%), Gaps = 30/612 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------KFSNISFH 253
                  I  E S ADL+ E    ++ E                        KF+ +   
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGK 235

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   E+ +
Sbjct: 236 FQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLV 295

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
           ++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QKL  +
Sbjct: 296 MKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMI 355

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  L +  ++DI+ +M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 356 EQETSLSVERIKDISHRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 415

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 416 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 475

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  
Sbjct: 476 RQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTT 535

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 536 LELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 595

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 596 RQIEAKALRKLR 607


>gi|319760203|ref|YP_004124141.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str. BVAF]
 gi|318038917|gb|ADV33467.1| RNA polymerase sigma factor [Candidatus Blochmannia vafer str. BVAF]
          Length = 620

 Score =  574 bits (1480), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 309/620 (49%), Positives = 421/620 (67%), Gaps = 24/620 (3%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLTFSE+ND L EDIID + + +II+    M I V E   D++
Sbjct: 4    NPQSQLKLLVTRGKEQGYLTFSEVNDHLSEDIIDSDQLHNIIQMMNDMGIQVMEEAPDSD 63

Query: 888  TLMLS---NITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 941
              +L+   +   ++D E+ATEAA   LS  D D GRT DP++MYM+EMG+VELLTR+GEI
Sbjct: 64   EFLLTKNCDTVVNNDEEDATEAAVQALSNTDPDLGRTTDPVRMYMKEMGAVELLTREGEI 123

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-KNFSSNNRV 1000
            +IAKRIE+G+  +  +++  P  I  +L    ++   E ++ +++ G +D  NF+ N   
Sbjct: 124  DIAKRIEDGINQVQCSVAEYPEAITYLLEQYQRVETGETRLSDLITGFVDLDNFNQNVET 183

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            I      N   +     +     E  E    ++ I        F  +RK +E      + 
Sbjct: 184  IPNITQQNIHHLSSNILTVTDDEENTENEDDDNSIDPELARKKFIALRKQYETTRQTIKY 243

Query: 1061 YIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
              + H+  S+E+L +       R   K  + L + +R+ ++++   E+ I+++ V+   M
Sbjct: 244  NGRNHDKSSSEILKLSEIFKQFRLVPKQFDYLVNNMRSMMDRIRFHERLIMKLCVDISKM 303

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQH-DYNLILCRNIPSIK-ELQQ---KLINLQTDIV 1168
            P+  FI +F  NE N  W+     IQ    N    + + ++  E+QQ   +L  ++ +  
Sbjct: 304  PKKKFIDLFSGNETNKAWL-----IQALSMNAGWAKKLDTVNAEVQQNIWQLYQIEKETG 358

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  +++INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 359  LTIEQVKNINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 418

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 419  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQ 478

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            ETG EP P  ++ +M + E+KIRK++KIAKEPVSME+P+GDDEDSHLGDFIED N+  P 
Sbjct: 479  ETGCEPTPEELSKRMLISEDKIRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPL 538

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A + ++++   D+L+ LTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEA
Sbjct: 539  DSATSDNLKAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEA 598

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   L+ FL+
Sbjct: 599  KALRKLRHPSRSEILRSFLD 618



 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 302/607 (49%), Positives = 412/607 (67%), Gaps = 24/607 (3%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLTFSE+ND L EDIID + + +II+    M I V E   D++
Sbjct: 4   NPQSQLKLLVTRGKEQGYLTFSEVNDHLSEDIIDSDQLHNIIQMMNDMGIQVMEEAPDSD 63

Query: 98  TLMLS---NITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEI 151
             +L+   +   ++D E+ATEAA   LS  D D GRT DP++MYM+EMG+VELLTR+GEI
Sbjct: 64  EFLLTKNCDTVVNNDEEDATEAAVQALSNTDPDLGRTTDPVRMYMKEMGAVELLTREGEI 123

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-KNFSSNNRV 210
           +IAKRIE+G+  +  +++  P  I  +L    ++   E ++ +++ G +D  NF+ N   
Sbjct: 124 DIAKRIEDGINQVQCSVAEYPEAITYLLEQYQRVETGETRLSDLITGFVDLDNFNQNVET 183

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           I      N   +     +     E  E    ++ I        F  +RK +E      + 
Sbjct: 184 IPNITQQNIHHLSSNILTVTDDEENTENEDDDNSIDPELARKKFIALRKQYETTRQTIKY 243

Query: 271 YIKAHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
             + H+  S+E+L +       R   K  + L + +R+ ++++   E+ I+++ V+   M
Sbjct: 244 NGRNHDKSSSEILKLSEIFKQFRLVPKQFDYLVNNMRSMMDRIRFHERLIMKLCVDISKM 303

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQH-DYNLILCRNIPSIK-ELQQ---KLINLQTDIV 378
           P+  FI +F  NE N  W+     IQ    N    + + ++  E+QQ   +L  ++ +  
Sbjct: 304 PKKKFIDLFSGNETNKAWL-----IQALSMNAGWAKKLDTVNAEVQQNIWQLYQIEKETG 358

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  +++INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 359 LTIEQVKNINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 418

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQ
Sbjct: 419 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQ 478

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           ETG EP P  ++ +M + E+KIRK++KIAKEPVSME+P+GDDEDSHLGDFIED N+  P 
Sbjct: 479 ETGCEPTPEELSKRMLISEDKIRKVLKIAKEPVSMETPIGDDEDSHLGDFIEDTNLDLPL 538

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A + ++++   D+L+ LTPRE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEA
Sbjct: 539 DSATSDNLKAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEA 598

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 599 KALRKLR 605


>gi|444331346|ref|ZP_21148854.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype a str. A160]
 gi|443552561|gb|ELT59850.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype a str. A160]
          Length = 616

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 415/614 (67%), Gaps = 13/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTGSETEELAE 181

Query: 1006 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
            + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182  DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242  GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302  KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482  SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSETLRSFLD 615



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 406/601 (67%), Gaps = 13/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTGSETEELAE 181

Query: 216 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
           + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182 DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242 GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302 KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482 SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|217974326|ref|YP_002359077.1| RNA polymerase sigma 70 subunit RpoD [Shewanella baltica OS223]
 gi|217499461|gb|ACK47654.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS223]
          Length = 611

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 309/612 (50%), Positives = 416/612 (67%), Gaps = 24/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
             +   +    D + ++ E  K     E+  +F  +   ++   K  + +G      +KA 
Sbjct: 188  LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIDAKGREHPESVKAL 247

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K F  N
Sbjct: 248  FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKFFTGN 307

Query: 1126 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308  ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479  EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 539  KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 598

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 599  PSRSEILKSFLD 610



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 301/599 (50%), Positives = 407/599 (67%), Gaps = 24/599 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D++ +     I    +  E
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEDVAPTATHIGSELSEEE 187

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
            +   +    D + ++ E  K     E+  +F  +   ++   K  + +G      +KA 
Sbjct: 188 LEDEDDEEDDDDTEDEEEGNKGPDPEEARERFGQLRTAYESALKIIDAKGREHPESVKAL 247

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ +L++ V +  MP+ +F+K F  N
Sbjct: 248 FEIGEIFKEFRLVPKQFDRLVKSMRTMMDRVRVQERLVLKLCVEQAKMPKKNFVKFFTGN 307

Query: 336 EINLNWVDNETKIQHDY---------NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           E NL+W + E      Y         ++I CR          KL  ++ +  L ++ ++D
Sbjct: 308 ETNLDWFNTEKASTKPYAEGLRMVEDDVIRCRT---------KLAAVEEETGLAISAIKD 358

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 359 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 418

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 419 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 478

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 479 EELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 538

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 539 KNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|262392398|ref|YP_003284252.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|451974347|ref|ZP_21926539.1| RNA polymerase sigma factor RpoD [Vibrio alginolyticus E0666]
 gi|262335992|gb|ACY49787.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|451930743|gb|EMD78445.1| RNA polymerase sigma factor RpoD [Vibrio alginolyticus E0666]
          Length = 620

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 316/621 (50%), Positives = 417/621 (67%), Gaps = 25/621 (4%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV---L 884
            N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E      
Sbjct: 4    NPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 63

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64   DLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +       
Sbjct: 123  KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTAT 181

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKM 1047
               +E   L ES   +   E ++  +                   +L KF+ +   +  +
Sbjct: 182  HIGSE---LTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNL 238

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            + A  + GYNS     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 239  QLAINEYGYNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSV 298

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 299  VEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEET 358

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 359  SLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 418

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 419  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 478

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 479  QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 538

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 539  LDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 598

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 599  AKALRKLRHPSRSETLRSFLD 619



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 408/608 (67%), Gaps = 25/608 (4%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV---L 94
           N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E      
Sbjct: 4   NPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 63

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 64  DLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +       
Sbjct: 123 KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTAT 181

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKM 257
              +E   L ES   +   E ++  +                   +L KF+ +   +  +
Sbjct: 182 HIGSE---LTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNL 238

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           + A  + GYNS     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 239 QLAINEYGYNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSV 298

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 299 VEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEET 358

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 359 SLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 418

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 419 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 478

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 479 QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 538

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 539 LDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 598

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 599 AKALRKLR 606


>gi|153801472|ref|ZP_01956058.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
 gi|124122963|gb|EAY41706.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-3]
          Length = 625

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
                   I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYAAKVREQEEEIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
                  I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYAAKVREQEEEIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|114048481|ref|YP_739031.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
 gi|113889923|gb|ABI43974.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. MR-7]
          Length = 619

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/608 (50%), Positives = 409/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 1008
              +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131  NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 1009 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +     +    +      +            E+  +F  +   ++   K  E +G     
Sbjct: 191  DLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYENALKIIEAKGREHPE 250

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             IKA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251  SIKALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311  FFTGNETNLDWFDAEKNSTKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 551  HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 610

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 611  EILKSFLD 618



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 400/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 218
             +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 219 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +     +    +      +            E+  +F  +   ++   K  E +G     
Sbjct: 191 DLDDEDDDEEDEDEDGDGDGDDDGNKGPDPEEARERFGQLRTAYENALKIIEAKGREHPE 250

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            IKA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251 SIKALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311 FFTGNETNLDWFDAEKNSTKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|85058229|ref|YP_453931.1| RNA polymerase sigma factor RpoD [Sodalis glossinidius str.
            'morsitans']
 gi|84778749|dbj|BAE73526.1| RNA polymerase sigma-70 factor RpoD [Sodalis glossinidius str.
            'morsitans']
          Length = 615

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 303/612 (49%), Positives = 408/612 (66%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTF+E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 1056
              +      I     +   +  +    +        +  KF  +   ++  R   +  G 
Sbjct: 183  IGSELSADEIADDDDEDEEDGDDDSTDDDNSIDPELARQKFVELREQYEITRNVIKTNGR 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +         N+S+     R   K  + L + +R  +++V   E+ I+++ V    MP+ 
Sbjct: 243  SHAKSASEILNLSDVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERLIMKLCVEISKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +F+ +F  NE + +W      +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303  NFVTLFAGNETSESWFKAALAMNKPWSEKLHEVDDDVYRSLQKLRQIEEETGLTIEQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 483  EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 296/599 (49%), Positives = 399/599 (66%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTF+E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTFAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETTSDTDEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAGEARLSDLITGFVDPNAEEDMAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGY 266
             +      I     +   +  +    +        +  KF  +   ++  R   +  G 
Sbjct: 183 IGSELSADEIADDDDEDEEDGDDDSTDDDNSIDPELARQKFVELREQYEITRNVIKTNGR 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +         N+S+     R   K  + L + +R  +++V   E+ I+++ V    MP+ 
Sbjct: 243 SHAKSASEILNLSDVFKQFRLVPKQFDYLVNNMRAMMDRVRTQERLIMKLCVEISKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +F+ +F  NE + +W      +   ++  L      +    QKL  ++ +  L +  ++D
Sbjct: 303 NFVTLFAGNETSESWFKAALAMNKPWSEKLHEVDDDVYRSLQKLRQIEEETGLTIEQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+
Sbjct: 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|147756|gb|AAA24601.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 613

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 299/610 (49%), Positives = 413/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   +++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 292/597 (48%), Positives = 404/597 (67%), Gaps = 8/597 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   +++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              D+L  LT RE+KVLRMRFGI+M++D+TLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|332288976|ref|YP_004419828.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
 gi|330431872|gb|AEC16931.1| RNA polymerase sigma factor RpoD [Gallibacterium anatis UMN179]
          Length = 624

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 309/633 (48%), Positives = 409/633 (64%), Gaps = 43/633 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K LI  GKE+GYLT++E+ND LPED++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLIAQGKEQGYLTYAEVNDSLPEDLVDADQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ N+T +D VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENVTDEDAVEEATQV-LSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK--- 1002
            RIEEG+ ++  A++  P  +  +L   D + K E+++ +++ G +D N        K   
Sbjct: 122  RIEEGINEVQCAVAEYPQALDHLLAQYDLVEKGEVRLSDLITGFVDPNAVDTEDYSKFMS 181

Query: 1003 ---------------------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLI 1035
                                          NN+ +     S   +++ E           
Sbjct: 182  DDSGEGEDDDNISSDDLDESDDDEDSDSESNNSADNDSDNSIDPEMARE----------- 230

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            KFS +     K   A +K G  ++      N +S      R   K  + L  ++R+ + +
Sbjct: 231  KFSALKEQHHKTVAAIDKYGRGNKKAKDQINALSEIFQQFRLVPKQFDILVLSMRDMMKR 290

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            +   E+QI  + V    MP+  F K F  +E N  W++       +++  L      I++
Sbjct: 291  IRTQERQIQRLAVEYAKMPKGTFQKAFIGHETNDAWIEKALAAGKNWSEKLKDYEDGIRQ 350

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
                L  ++ +  L +  +R I  K+  GE+KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 351  AIALLKVIEQESGLTITQIRQIGEKISQGELKARRAKKEMVEANLRLVISIAKKYTNRGL 410

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 411  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 470

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 471  INKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHL 530

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 531  GDFIEDNTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQ 590

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            FDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  FDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 623



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 302/620 (48%), Positives = 400/620 (64%), Gaps = 43/620 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K LI  GKE+GYLT++E+ND LPED++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLIAQGKEQGYLTYAEVNDSLPEDLVDADQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ N+T +D VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENVTDEDAVEEATQV-LSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK--- 212
           RIEEG+ ++  A++  P  +  +L   D + K E+++ +++ G +D N        K   
Sbjct: 122 RIEEGINEVQCAVAEYPQALDHLLAQYDLVEKGEVRLSDLITGFVDPNAVDTEDYSKFMS 181

Query: 213 ---------------------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLI 245
                                         NN+ +     S   +++ E           
Sbjct: 182 DDSGEGEDDDNISSDDLDESDDDEDSDSESNNSADNDSDNSIDPEMARE----------- 230

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           KFS +     K   A +K G  ++      N +S      R   K  + L  ++R+ + +
Sbjct: 231 KFSALKEQHHKTVAAIDKYGRGNKKAKDQINALSEIFQQFRLVPKQFDILVLSMRDMMKR 290

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           +   E+QI  + V    MP+  F K F  +E N  W++       +++  L      I++
Sbjct: 291 IRTQERQIQRLAVEYAKMPKGTFQKAFIGHETNDAWIEKALAAGKNWSEKLKDYEDGIRQ 350

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
               L  ++ +  L +  +R I  K+  GE+KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 351 AIALLKVIEQESGLTITQIRQIGEKISQGELKARRAKKEMVEANLRLVISIAKKYTNRGL 410

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 411 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 470

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 471 INKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHL 530

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 531 GDFIEDNTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQ 590

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 591 FDVTRERIRQIEAKALRKLR 610


>gi|416077262|ref|ZP_11585806.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. SCC1398]
 gi|444338461|ref|ZP_21152296.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. SCC4092]
 gi|348004059|gb|EGY44590.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. SCC1398]
 gi|443545019|gb|ELT54889.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. SCC4092]
          Length = 616

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 415/614 (67%), Gaps = 13/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLITQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 1006 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
            + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182  DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242  GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302  KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482  SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSETLRSFLD 615



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 406/601 (67%), Gaps = 13/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLITQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 216 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
           + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182 DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242 GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302 KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482 SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|387121505|ref|YP_006287388.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans D7S-1]
 gi|415754433|ref|ZP_11480649.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans D17P-3]
 gi|416035201|ref|ZP_11573485.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype a str. H5P1]
 gi|416043829|ref|ZP_11574790.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype d str. I63B]
 gi|416066326|ref|ZP_11581993.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans serotype f str. D18P1]
 gi|429733420|ref|ZP_19267640.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans Y4]
 gi|347996821|gb|EGY37873.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype d str. I63B]
 gi|347997500|gb|EGY38491.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype a str. H5P1]
 gi|348002922|gb|EGY43585.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans serotype f str. D18P1]
 gi|348656216|gb|EGY71613.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans D17P-3]
 gi|385875997|gb|AFI87556.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans D7S-1]
 gi|429154897|gb|EKX97606.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans Y4]
          Length = 616

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 415/614 (67%), Gaps = 13/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 1006 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
            + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182  DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242  GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302  KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482  SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSETLRSFLD 615



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 406/601 (67%), Gaps = 13/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 216 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
           + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182 DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242 GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302 KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482 SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|254229773|ref|ZP_04923181.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269968567|ref|ZP_06182570.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
 gi|151937740|gb|EDN56590.1| sigma-70, non-essential region family [Vibrio sp. Ex25]
 gi|269826825|gb|EEZ81156.1| RNA polymerase sigma factor [Vibrio alginolyticus 40B]
          Length = 639

 Score =  574 bits (1479), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 316/621 (50%), Positives = 417/621 (67%), Gaps = 25/621 (4%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV---L 884
            N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E      
Sbjct: 23   NPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 82

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 83   DLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +       
Sbjct: 142  KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTAT 200

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKM 1047
               +E   L ES   +   E ++  +                   +L KF+ +   +  +
Sbjct: 201  HIGSE---LTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNL 257

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            + A  + GYNS     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 258  QLAINEYGYNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSV 317

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 318  VEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEET 377

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 378  SLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 437

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 438  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 497

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 498  QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 557

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 558  LDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 617

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 618  AKALRKLRHPSRSETLRSFLD 638



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 408/608 (67%), Gaps = 25/608 (4%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV---L 94
           N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E      
Sbjct: 23  NPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDAD 82

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 83  DLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 141

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +       
Sbjct: 142 KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTAT 200

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDKM 257
              +E   L ES   +   E ++  +                   +L KF+ +   +  +
Sbjct: 201 HIGSE---LTESQLEEEDDEDVDDDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNL 257

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           + A  + GYNS     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 258 QLAINEYGYNSPKATVANEMMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSV 317

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 318 VEYGKMPKKSFIALFTGNESSEAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEET 377

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 378 SLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 437

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 497

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 498 QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 557

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 558 LDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 617

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 618 AKALRKLR 625


>gi|28897178|ref|NP_796783.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
            2210633]
 gi|153839257|ref|ZP_01991924.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|260361470|ref|ZP_05774529.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|260878083|ref|ZP_05890438.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|260896978|ref|ZP_05905474.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio parahaemolyticus
            Peru-466]
 gi|260902497|ref|ZP_05910892.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|417321267|ref|ZP_12107807.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus 10329]
 gi|433656701|ref|YP_007274080.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus BB22OP]
 gi|28805387|dbj|BAC58667.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus RIMD
            2210633]
 gi|149747222|gb|EDM58210.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ3810]
 gi|308088714|gb|EFO38409.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio parahaemolyticus
            Peru-466]
 gi|308089726|gb|EFO39421.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AN-5034]
 gi|308109810|gb|EFO47350.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus AQ4037]
 gi|308110993|gb|EFO48533.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus K5030]
 gi|328471947|gb|EGF42824.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus 10329]
 gi|432507389|gb|AGB08906.1| RNA polymerase sigma factor RpoD [Vibrio parahaemolyticus BB22OP]
          Length = 620

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/618 (50%), Positives = 418/618 (67%), Gaps = 17/618 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF---SSNNRV 1000
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +    ++    
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTAT 181

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE----------SLIKFSNISFHFDKMRKA 1050
              G++ +  +    +    +   E  +               +L KF+ +   +  ++ A
Sbjct: 182  HIGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQNLQLA 241

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
              + GY+S     A+  + +     R T K  + L + LR  +++V   E+ I++ VV  
Sbjct: 242  INEYGYDSPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEY 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +  L 
Sbjct: 302  GKMPKKSFIALFTGNESSDAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLN 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  VQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+
Sbjct: 482  GREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 541

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542  ATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FL+
Sbjct: 602  LRKLRHPSRSETLRSFLD 619



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/605 (50%), Positives = 409/605 (67%), Gaps = 17/605 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF---SSNNRV 210
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +    ++    
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTAT 181

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE----------SLIKFSNISFHFDKMRKA 260
             G++ +  +    +    +   E  +               +L KF+ +   +  ++ A
Sbjct: 182 HIGSELSETQLEEEDEEDLEDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQNLQLA 241

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
             + GY+S     A+  + +     R T K  + L + LR  +++V   E+ I++ VV  
Sbjct: 242 INEYGYDSPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEY 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +  L 
Sbjct: 302 GKMPKKSFIALFTGNESSDAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLN 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 VQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+
Sbjct: 482 GREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 541

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542 ATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 621 LRKLR 625
           LRKLR
Sbjct: 602 LRKLR 606


>gi|381160983|ref|ZP_09870215.1| RNA polymerase sigma factor, sigma-70 family [Thiorhodovibrio sp.
            970]
 gi|380879047|gb|EIC21139.1| RNA polymerase sigma factor, sigma-70 family [Thiorhodovibrio sp.
            970]
          Length = 606

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 306/600 (51%), Positives = 413/600 (68%), Gaps = 8/600 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GK++G+LT++E+ND LP+ I++ E IE I++    M I+V E        + 
Sbjct: 10   QLKQLIAKGKDQGFLTYTEVNDHLPDGIVEPEQIEDIVRMINDMGITVHETAPSEVDQLS 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
             +  +DD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIEEGL
Sbjct: 70   DSAVADDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIAKRIEEGL 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK---NNN 1008
              ++ A+S  P T+  +L   ++  + EI+I +++ G  D +      + KG     N +
Sbjct: 130  NQVLQALSLYPKTVGMLLELIEQAEREEIRITDVISGFDDGSDEIAQPINKGAAKEVNGD 189

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 1068
             E    E+   D   +  E  +    ++ S     ++++       G + +    A   +
Sbjct: 190  AESSEEEAEVIDTGPDPEEFAQRAKALRDS-----YERLILCLHDYGRDDDRTRYAGERV 244

Query: 1069 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 1128
            S E LG +  A     L   LR  I ++   E+ I+ + ++   MPR  FI  FP+NE N
Sbjct: 245  SEEFLGFKLVAGVFNDLIRVLRQTIERIRAQERHIMGLCIDGARMPRKVFIDSFPDNETN 304

Query: 1129 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
              W+D        Y   L      ++  Q++L+ L+ + VL ++++++INRKM  GE KA
Sbjct: 305  AGWLDQHLASSAKYAGRLGEYAEEVRRAQRRLMELEEENVLSISEIKEINRKMSIGEAKA 364

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 365  RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 424

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +MEMPE+
Sbjct: 425  WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMVQEMGREATPEELAERMEMPED 484

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT
Sbjct: 485  KVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTVISPVDSATAEGLREATQNMLASLT 544

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  KL+ F++
Sbjct: 545  SREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKLRSFID 604



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 303/595 (50%), Positives = 406/595 (68%), Gaps = 9/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GK++G+LT++E+ND LP+ I++ E IE I++    M I+V E        + 
Sbjct: 10  QLKQLIAKGKDQGFLTYTEVNDHLPDGIVEPEQIEDIVRMINDMGITVHETAPSEVDQLS 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
            +  +DD+  EA  AAL++VDS+FGRT DP++MYMREMG+VELLTR+GE+ IAKRIEEGL
Sbjct: 70  DSAVADDEAAEAAAAALASVDSEFGRTTDPVRMYMREMGTVELLTREGELRIAKRIEEGL 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK---NNN 218
             ++ A+S  P T+  +L   ++  + EI+I +++ G  D +      + KG     N +
Sbjct: 130 NQVLQALSLYPKTVGMLLELIEQAEREEIRITDVISGFDDGSDEIAQPINKGAAKEVNGD 189

Query: 219 EEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278
            E    E+   D   +  E  +    ++ S     ++++       G + +    A   +
Sbjct: 190 AESSEEEAEVIDTGPDPEEFAQRAKALRDS-----YERLILCLHDYGRDDDRTRYAGERV 244

Query: 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEIN 338
           S E LG +  A     L   LR  I ++   E+ I+ + ++   MPR  FI  FP+NE N
Sbjct: 245 SEEFLGFKLVAGVFNDLIRVLRQTIERIRAQERHIMGLCIDGARMPRKVFIDSFPDNETN 304

Query: 339 LNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
             W+D        Y   L      ++  Q++L+ L+ + VL ++++++INRKM  GE KA
Sbjct: 305 AGWLDQHLASSAKYAGRLGEYAEEVRRAQRRLMELEEENVLSISEIKEINRKMSIGEAKA 364

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT
Sbjct: 365 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 424

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ++QE G E  P  +A +MEMPE+
Sbjct: 425 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMVQEMGREATPEELAERMEMPED 484

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +++P D+A    +R   +++L SLT
Sbjct: 485 KVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTVISPVDSATAEGLREATQNMLASLT 544

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
            RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 545 SREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDKL 599


>gi|237809411|ref|YP_002893851.1| RNA polymerase sigma-70 subunit RpoD [Tolumonas auensis DSM 9187]
 gi|237501672|gb|ACQ94265.1| RNA polymerase, sigma 70 subunit, RpoD [Tolumonas auensis DSM 9187]
          Length = 617

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/608 (49%), Positives = 411/608 (67%), Gaps = 9/608 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+V D + L
Sbjct: 9    QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENVPDADDL 68

Query: 890  MLSNITSDDDVEEATEA-ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            +L+   + DD      A  L++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 69   LLTENNAADDDAAEAAAQVLASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 128

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
            +G+  +  +++  P  I  +L   D+     I++ +I+ G + ++              +
Sbjct: 129  DGINQVQSSVAEYPEAITYLLDQFDRFEAGHIRLGDIISGFVSEDDDLPPTATNIGSALD 188

Query: 1009 EEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            EE +  + +  +   E  +    E        +  KFS +   ++  R A +  G +S+ 
Sbjct: 189  EETLKADDTDDEDEDEDGDDDAEEDTGPDPEVAREKFSALRTQYEITRDAIKANGRDSDL 248

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                   ++N     R   K  ++L +++R  + +V   E+ IL   V    MP+ +F+ 
Sbjct: 249  AKVQILELANVFKEFRLVPKQFDRLVNSMREMMERVRVQERLILRYCVEYAKMPKKNFVT 308

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  NE +  W +        ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 309  AFTNNESSNGWFEFAKSSGKPWSTALANMDEDVQRSIQKLQQVEQETGLSIAQIKDINRR 368

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 369  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 428

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A
Sbjct: 429  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELA 488

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+++  
Sbjct: 489  ERMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLKAAT 548

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 549  RDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 608

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 609  EVLRSFLD 616



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 294/595 (49%), Positives = 402/595 (67%), Gaps = 9/595 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+V D + L
Sbjct: 9   QSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENVPDADDL 68

Query: 100 MLSNITSDDDVEEATEA-ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           +L+   + DD      A  L++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 69  LLTENNAADDDAAEAAAQVLASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 128

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
           +G+  +  +++  P  I  +L   D+     I++ +I+ G + ++              +
Sbjct: 129 DGINQVQSSVAEYPEAITYLLDQFDRFEAGHIRLGDIISGFVSEDDDLPPTATNIGSALD 188

Query: 219 EEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNSES 270
           EE +  + +  +   E  +    E        +  KFS +   ++  R A +  G +S+ 
Sbjct: 189 EETLKADDTDDEDEDEDGDDDAEEDTGPDPEVAREKFSALRTQYEITRDAIKANGRDSDL 248

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                  ++N     R   K  ++L +++R  + +V   E+ IL   V    MP+ +F+ 
Sbjct: 249 AKVQILELANVFKEFRLVPKQFDRLVNSMREMMERVRVQERLILRYCVEYAKMPKKNFVT 308

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  NE +  W +        ++  L      ++   QKL  ++ +  L +  ++DINR+
Sbjct: 309 AFTNNESSNGWFEFAKSSGKPWSTALANMDEDVQRSIQKLQQVEQETGLSIAQIKDINRR 368

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 369 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 428

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  +A
Sbjct: 429 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEELA 488

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+++  
Sbjct: 489 ERMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLKAAT 548

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 RDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|397163890|ref|ZP_10487348.1| RNA polymerase sigma factor rpoD [Enterobacter radicincitans DSM
            16656]
 gi|396094445|gb|EJI91997.1| RNA polymerase sigma factor rpoD [Enterobacter radicincitans DSM
            16656]
          Length = 614

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 415/611 (67%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETTADTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G +D N   +      +
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEQARLSDLITGFVDPNAEEDLAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
              +      ++    D   +  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183  VGSELSSEEMDDDDDDEDEDDDDSSDDDNSIDPELAREKFGELRTQYELTRDTIKAKGRS 242

Query: 1065 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            H     E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243  HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303  FITLFTGNETSETWFNAALAMNKPWSEKLHEVTEEVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
            +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSEVLRSFLD 613



 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 406/598 (67%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  T+D D + A  A   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETTADTDDDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G +D N   +      +
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEQARLSDLITGFVDPNAEEDLAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
             +      ++    D   +  +    ++ I        F ++R  +E      ++  ++
Sbjct: 183 VGSELSSEEMDDDDDDEDEDDDDSSDDDNSIDPELAREKFGELRTQYELTRDTIKAKGRS 242

Query: 275 HNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           H     E+L +       R   K  + L +++R  +++V   E+ I+++ V +C MP+ +
Sbjct: 243 HAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRIMMDRVRTQERIIMKLCVEQCKMPKKN 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W +    +   ++  L      ++   QKL  ++ +  L +  ++DI
Sbjct: 303 FITLFTGNETSETWFNAALAMNKPWSEKLHEVTEEVQRSLQKLQQIEEETGLTIEQVKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 AATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|15603106|ref|NP_246178.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. Pm70]
 gi|12721597|gb|AAK03325.1| RpoD [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 622

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/623 (49%), Positives = 419/623 (67%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  + + V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTESDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
              + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 410/610 (67%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  + + V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTESDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
             + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|336312458|ref|ZP_08567407.1| RNA polymerase sigma factor RpoD [Shewanella sp. HN-41]
 gi|335863964|gb|EGM69082.1| RNA polymerase sigma factor RpoD [Shewanella sp. HN-41]
          Length = 614

 Score =  573 bits (1478), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 307/606 (50%), Positives = 412/606 (67%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 128  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 187

Query: 1010 EKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            +    +    D      +           E+  +FS +   ++   K  E +G      +
Sbjct: 188  DLDDEDDEDEDDEESGDDDDDGNKGPDPEEARERFSQLRTAYENALKIIEAKGREHPESV 247

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            KA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K F
Sbjct: 248  KALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLVMKLCVEQAKMPKKNFVKFF 307

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              NE NL+W   E      Y   L      +   + KL  ++ +  L +  ++DINR+M 
Sbjct: 308  TGNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAIAAIKDINRRMS 367

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   +
Sbjct: 488  MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHE 547

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 548  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEI 607

Query: 1423 LKIFLE 1428
            LK FL+
Sbjct: 608  LKSFLD 613



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 299/593 (50%), Positives = 403/593 (67%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 187

Query: 220 EKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           +    +    D      +           E+  +FS +   ++   K  E +G      +
Sbjct: 188 DLDDEDDEDEDDEESGDDDDDGNKGPDPEEARERFSQLRTAYENALKIIEAKGREHPESV 247

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           KA   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K F
Sbjct: 248 KALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLVMKLCVEQAKMPKKNFVKFF 307

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             NE NL+W   E      Y   L      +   + KL  ++ +  L +  ++DINR+M 
Sbjct: 308 TGNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAIAAIKDINRRMS 367

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   +
Sbjct: 488 MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHE 547

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|330831100|ref|YP_004394052.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|406675679|ref|ZP_11082866.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AMC35]
 gi|423203623|ref|ZP_17190201.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AER39]
 gi|423203988|ref|ZP_17190544.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AMC34]
 gi|423208255|ref|ZP_17194809.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AER397]
 gi|328806236|gb|AEB51435.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|404612918|gb|EKB09975.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AER39]
 gi|404619302|gb|EKB16218.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AER397]
 gi|404627069|gb|EKB23875.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AMC35]
 gi|404627982|gb|EKB24770.1| RNA polymerase sigma factor rpoD [Aeromonas veronii AMC34]
          Length = 618

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 413/610 (67%), Gaps = 13/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            +  +  +++  P  I  +L   DK    ++++ +I+ G ID N + +      +  +   
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETEDMAPTATHIGSELG 187

Query: 1011 KILIESSSADLSTEQLEKLKYESLI------------KFSNISFHFDKMRKAFEKEGYNS 1058
            +  +     +   ++ E                    KF  +   ++  R + +K G   
Sbjct: 188  EDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEVTRLSIQKNGRAH 247

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F
Sbjct: 248  EDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTF 307

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +  F  NE    W + + +    ++  L      I+    KL  ++ +  L +  ++DIN
Sbjct: 308  VAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDIQRAIGKLQQIEEETGLSIAQIKDIN 367

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 368  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 427

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  
Sbjct: 428  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEE 487

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+R+
Sbjct: 488  LAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRN 547

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 548  ATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 607

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 608  RSEVLRSFLD 617



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 293/597 (49%), Positives = 404/597 (67%), Gaps = 13/597 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           +  +  +++  P  I  +L   DK    ++++ +I+ G ID N + +      +  +   
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETEDMAPTATHIGSELG 187

Query: 221 KILIESSSADLSTEQLEKLKYESLI------------KFSNISFHFDKMRKAFEKEGYNS 268
           +  +     +   ++ E                    KF  +   ++  R + +K G   
Sbjct: 188 EDDLADEDEEDEEDEDEDGDSSDDDGDGGPDPEVAREKFGELRAQYEVTRLSIQKNGRAH 247

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F
Sbjct: 248 EDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTF 307

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           +  F  NE    W + + +    ++  L      I+    KL  ++ +  L +  ++DIN
Sbjct: 308 VAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDIQRAIGKLQQIEEETGLSIAQIKDIN 367

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 368 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 427

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P  
Sbjct: 428 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNPEE 487

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+R+
Sbjct: 488 LAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESLRN 547

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 ATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|365967986|ref|YP_004949548.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans ANH9381]
 gi|416081183|ref|ZP_11586382.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. I23C]
 gi|444347701|ref|ZP_21155532.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. S23A]
 gi|348011098|gb|EGY51085.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. I23C]
 gi|365746899|gb|AEW77804.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans ANH9381]
 gi|443548345|gb|ELT57617.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype b str. S23A]
          Length = 616

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 415/614 (67%), Gaps = 13/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 1006 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
            + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182  DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNNVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242  GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302  KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482  SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSETLRSFLD 615



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 406/601 (67%), Gaps = 13/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +   +  +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEELAE 181

Query: 216 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
           + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182 DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNNVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242 GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302 KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482 SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|442608717|ref|ZP_21023464.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas luteoviolacea B =
            ATCC 29581]
 gi|441750113|emb|CCQ09526.1| RNA polymerase sigma factor RpoD [Pseudoalteromonas luteoviolacea B =
            ATCC 29581]
          Length = 618

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 315/621 (50%), Positives = 413/621 (66%), Gaps = 33/621 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I+V+E+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGITVAENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+DDD  EA  AAL+TVD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDDDAAEAAAAALATVDKEIGRTTDPVRMYMREMGTVELLTREGEILIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN---- 1007
              +  +++  P  I E+L   DK    EI++ +IV G  D N    +     +  +    
Sbjct: 128  NQVQLSVAEYPEAIAELLEQWDKFEAEEIRLSDIVSGFYDPNALEEDEGFPISATHVGSE 187

Query: 1008 ------------------NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                              ++          +++ E  EKL+             ++  R+
Sbjct: 188  LSDDDLDDEDDDGDDDDSDDSDDGDSGPDPEVAREHFEKLRA-----------LYNHARE 236

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
             FE +G +     +A  +I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 237  VFETKGRSHPDADQAIQDIGELFRMFKLVPKQFDRMVNNMRAMMDKVRVQERIIMKQAVQ 296

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
               +P+  F+K F  NE ++ W+D E      Y+  L    P I+    KL  ++    L
Sbjct: 297  VAKVPKKTFVKHFANNETDMAWIDAEISAGEKYSEKLEEVRPEIERCINKLKAIEESTGL 356

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
             +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 357  TVERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 416

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 417  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 476

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 477  MGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPID 536

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
            +A   S+R+   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 537  SATMESLRAATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 596

Query: 1410 ALRKLRHPSRYYKLKIFLEGK 1430
            ALRKLRHPSR   LK FL+ K
Sbjct: 597  ALRKLRHPSRSDLLKSFLDIK 617



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 309/614 (50%), Positives = 406/614 (66%), Gaps = 34/614 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I+V+E+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGITVAENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+DDD  EA  AAL+TVD + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDDDAAEAAAAALATVDKEIGRTTDPVRMYMREMGTVELLTREGEILIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN---- 217
             +  +++  P  I E+L   DK    EI++ +IV G  D N    +     +  +    
Sbjct: 128 NQVQLSVAEYPEAIAELLEQWDKFEAEEIRLSDIVSGFYDPNALEEDEGFPISATHVGSE 187

Query: 218 ------------------NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                             ++          +++ E  EKL+             ++  R+
Sbjct: 188 LSDDDLDDEDDDGDDDDSDDSDDGDSGPDPEVAREHFEKLRA-----------LYNHARE 236

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
            FE +G +     +A  +I       +   K  +++ + +R  +++V   E+ I++  V 
Sbjct: 237 VFETKGRSHPDADQAIQDIGELFRMFKLVPKQFDRMVNNMRAMMDKVRVQERIIMKQAVQ 296

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
              +P+  F+K F  NE ++ W+D E      Y+  L    P I+    KL  ++    L
Sbjct: 297 VAKVPKKTFVKHFANNETDMAWIDAEISAGEKYSEKLEEVRPEIERCINKLKAIEESTGL 356

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
            +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 357 TVERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 416

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE
Sbjct: 417 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 476

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D
Sbjct: 477 MGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPID 536

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
           +A   S+R+   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 537 SATMESLRAATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 596

Query: 620 ALRKLR-PLAHDWL 632
           ALRKLR P   D L
Sbjct: 597 ALRKLRHPSRSDLL 610


>gi|417823644|ref|ZP_12470236.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE48]
 gi|340048273|gb|EGR09195.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE48]
          Length = 625

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
                   I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEAGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
                  I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEAGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|15640541|ref|NP_230168.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
            str. N16961]
 gi|121728933|ref|ZP_01681939.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|153819447|ref|ZP_01972114.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|153822185|ref|ZP_01974852.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|227080700|ref|YP_002809251.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254291201|ref|ZP_04961997.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|254850756|ref|ZP_05240106.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255744255|ref|ZP_05418208.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
 gi|360037141|ref|YP_004938904.1| RNA polymerase primary sigma factor [Vibrio cholerae O1 str.
            2010EL-1786]
 gi|379740389|ref|YP_005332358.1| RNA polymerase sigma factor RpoD [Vibrio cholerae IEC224]
 gi|417812487|ref|ZP_12459147.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-49A2]
 gi|417815349|ref|ZP_12461983.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HCUF01]
 gi|417819377|ref|ZP_12465994.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE39]
 gi|418331492|ref|ZP_12942434.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-06A1]
 gi|418336367|ref|ZP_12945266.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-23A1]
 gi|418342748|ref|ZP_12949546.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-28A1]
 gi|418347911|ref|ZP_12952647.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-43A1]
 gi|418354374|ref|ZP_12957098.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-61A1]
 gi|419824993|ref|ZP_14348499.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CP1033(6)]
 gi|419829066|ref|ZP_14352555.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-1A2]
 gi|419831846|ref|ZP_14355313.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-61A2]
 gi|419835443|ref|ZP_14358888.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-46B1]
 gi|421315959|ref|ZP_15766531.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1032(5)]
 gi|421319290|ref|ZP_15769849.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1038(11)]
 gi|421323338|ref|ZP_15773867.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1041(14)]
 gi|421327743|ref|ZP_15778259.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1042(15)]
 gi|421330750|ref|ZP_15781232.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1046(19)]
 gi|421334332|ref|ZP_15784801.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1048(21)]
 gi|421342237|ref|ZP_15792644.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-43B1]
 gi|421346540|ref|ZP_15796923.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-46A1]
 gi|421353331|ref|ZP_15803664.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-45]
 gi|422305926|ref|ZP_16393113.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CP1035(8)]
 gi|422890562|ref|ZP_16932978.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-40A1]
 gi|422901429|ref|ZP_16936797.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-48A1]
 gi|422905645|ref|ZP_16940496.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-70A1]
 gi|422912249|ref|ZP_16946776.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HFU-02]
 gi|422916232|ref|ZP_16950573.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-02A1]
 gi|422921747|ref|ZP_16954954.1| RNA polymerase sigma factor rpoD [Vibrio cholerae BJG-01]
 gi|422924728|ref|ZP_16957762.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-38A1]
 gi|423144052|ref|ZP_17131667.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-19A1]
 gi|423148756|ref|ZP_17136116.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-21A1]
 gi|423152547|ref|ZP_17139746.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-22A1]
 gi|423155329|ref|ZP_17142466.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-32A1]
 gi|423159189|ref|ZP_17146162.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-33A2]
 gi|423163875|ref|ZP_17150664.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-48B2]
 gi|423730002|ref|ZP_17703321.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-17A1]
 gi|423733806|ref|ZP_17707022.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-41B1]
 gi|423747370|ref|ZP_17711397.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-50A2]
 gi|423816190|ref|ZP_17715176.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-55C2]
 gi|423848253|ref|ZP_17718962.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-59A1]
 gi|423878832|ref|ZP_17722570.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-60A1]
 gi|423891721|ref|ZP_17725412.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-62A1]
 gi|423926498|ref|ZP_17730027.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-77A1]
 gi|423946534|ref|ZP_17733442.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HE-40]
 gi|423975972|ref|ZP_17736989.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HE-46]
 gi|423996652|ref|ZP_17739918.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-02C1]
 gi|424001053|ref|ZP_17744143.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-17A2]
 gi|424005213|ref|ZP_17748198.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-37A1]
 gi|424008090|ref|ZP_17751040.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-44C1]
 gi|424015353|ref|ZP_17755203.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-55B2]
 gi|424018464|ref|ZP_17758266.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-59B1]
 gi|424023222|ref|ZP_17762887.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-62B1]
 gi|424026024|ref|ZP_17765641.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-69A1]
 gi|424585428|ref|ZP_18025022.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1030(3)]
 gi|424589767|ref|ZP_18029214.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1037(10)]
 gi|424594047|ref|ZP_18033386.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1040(13)]
 gi|424597984|ref|ZP_18037184.1| RNA polymerase sigma factor rpoD [Vibrio Cholerae CP1044(17)]
 gi|424600745|ref|ZP_18039902.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1047(20)]
 gi|424605639|ref|ZP_18044605.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1050(23)]
 gi|424609477|ref|ZP_18048336.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-39A1]
 gi|424612278|ref|ZP_18051086.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-41A1]
 gi|424616154|ref|ZP_18054846.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-42A1]
 gi|424620914|ref|ZP_18059444.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-47A1]
 gi|424623834|ref|ZP_18062314.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-50A1]
 gi|424628410|ref|ZP_18066719.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-51A1]
 gi|424632369|ref|ZP_18070488.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-52A1]
 gi|424635454|ref|ZP_18073478.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-55A1]
 gi|424639368|ref|ZP_18077267.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-56A1]
 gi|424644012|ref|ZP_18081767.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-56A2]
 gi|424647528|ref|ZP_18085208.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-57A1]
 gi|424651657|ref|ZP_18089182.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-57A2]
 gi|424655604|ref|ZP_18092907.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-81A2]
 gi|429887706|ref|ZP_19369216.1| RNA polymerase sigma factor RpoD [Vibrio cholerae PS15]
 gi|440708727|ref|ZP_20889388.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 4260B]
 gi|443502553|ref|ZP_21069543.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-64A1]
 gi|443506463|ref|ZP_21073256.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-65A1]
 gi|443510572|ref|ZP_21077238.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-67A1]
 gi|443514131|ref|ZP_21080673.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-68A1]
 gi|443517945|ref|ZP_21084364.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-71A1]
 gi|443522813|ref|ZP_21089055.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-72A2]
 gi|443526387|ref|ZP_21092470.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-78A1]
 gi|443530430|ref|ZP_21096446.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-7A1]
 gi|443534206|ref|ZP_21100120.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-80A1]
 gi|443537784|ref|ZP_21103641.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-81A1]
 gi|449054253|ref|ZP_21732921.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 str. Inaba
            G4222]
 gi|9654945|gb|AAF93687.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 biovar El Tor
            str. N16961]
 gi|121628781|gb|EAX61245.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V52]
 gi|126510018|gb|EAZ72612.1| RNA polymerase sigma factor RpoD [Vibrio cholerae NCTC 8457]
 gi|126520320|gb|EAZ77543.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|150422895|gb|EDN14846.1| RNA polymerase sigma factor RpoD [Vibrio cholerae AM-19226]
 gi|220897845|dbj|BAH11107.1| RNA polymerase sigma factor [Vibrio cholerae O1 biovar El tor]
 gi|227008588|gb|ACP04800.1| RNA polymerase sigma factor RpoD [Vibrio cholerae M66-2]
 gi|254846461|gb|EET24875.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MO10]
 gi|255738195|gb|EET93587.1| RNA polymerase sigma factor RpoD [Vibrio cholera CIRS 101]
 gi|340041233|gb|EGR02200.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE39]
 gi|340043335|gb|EGR04294.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HCUF01]
 gi|340043867|gb|EGR04824.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-49A2]
 gi|341625431|gb|EGS50884.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-70A1]
 gi|341626574|gb|EGS51945.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-48A1]
 gi|341627082|gb|EGS52410.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-40A1]
 gi|341640752|gb|EGS65331.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-02A1]
 gi|341641029|gb|EGS65601.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HFU-02]
 gi|341647962|gb|EGS72030.1| RNA polymerase sigma factor rpoD [Vibrio cholerae BJG-01]
 gi|341648556|gb|EGS72608.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-38A1]
 gi|356420519|gb|EHH74038.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-06A1]
 gi|356421694|gb|EHH75186.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-21A1]
 gi|356426185|gb|EHH79509.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-19A1]
 gi|356433148|gb|EHH86341.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-23A1]
 gi|356434713|gb|EHH87887.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-22A1]
 gi|356437966|gb|EHH91031.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-28A1]
 gi|356443147|gb|EHH95976.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-32A1]
 gi|356448022|gb|EHI00807.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-43A1]
 gi|356450316|gb|EHI03045.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-33A2]
 gi|356454150|gb|EHI06805.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-61A1]
 gi|356456394|gb|EHI09000.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-48B2]
 gi|356648295|gb|AET28350.1| RNA polymerase primary sigma factor [Vibrio cholerae O1 str.
            2010EL-1786]
 gi|378793899|gb|AFC57370.1| RNA polymerase sigma factor RpoD [Vibrio cholerae IEC224]
 gi|395922700|gb|EJH33516.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1032(5)]
 gi|395923183|gb|EJH33995.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1041(14)]
 gi|395925615|gb|EJH36412.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1038(11)]
 gi|395931477|gb|EJH42222.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1042(15)]
 gi|395934603|gb|EJH45341.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1046(19)]
 gi|395937441|gb|EJH48155.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1048(21)]
 gi|395945740|gb|EJH56405.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-43B1]
 gi|395946688|gb|EJH57348.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-46A1]
 gi|395954678|gb|EJH65287.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-45]
 gi|395962928|gb|EJH73216.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-56A2]
 gi|395963816|gb|EJH74068.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-57A2]
 gi|395966645|gb|EJH76760.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-42A1]
 gi|395975537|gb|EJH85026.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-47A1]
 gi|395977571|gb|EJH86976.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1030(3)]
 gi|395978965|gb|EJH88329.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1047(20)]
 gi|408009739|gb|EKG47634.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-39A1]
 gi|408016119|gb|EKG53675.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-50A1]
 gi|408016619|gb|EKG54153.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-41A1]
 gi|408021207|gb|EKG58472.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-52A1]
 gi|408027075|gb|EKG64058.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-56A1]
 gi|408027624|gb|EKG64586.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-55A1]
 gi|408036456|gb|EKG72886.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1037(10)]
 gi|408037003|gb|EKG73411.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-57A1]
 gi|408037185|gb|EKG73585.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1040(13)]
 gi|408044857|gb|EKG80743.1| RNA polymerase sigma factor rpoD [Vibrio Cholerae CP1044(17)]
 gi|408046752|gb|EKG82421.1| RNA polymerase sigma factor rpoD [Vibrio cholerae CP1050(23)]
 gi|408057380|gb|EKG92231.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-81A2]
 gi|408058911|gb|EKG93687.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-51A1]
 gi|408611264|gb|EKK84625.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CP1033(6)]
 gi|408622255|gb|EKK95243.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-1A2]
 gi|408627378|gb|EKL00190.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-17A1]
 gi|408627827|gb|EKL00620.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CP1035(8)]
 gi|408631809|gb|EKL04332.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-41B1]
 gi|408636861|gb|EKL08983.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-55C2]
 gi|408641963|gb|EKL13726.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-50A2]
 gi|408644126|gb|EKL15832.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-60A1]
 gi|408645238|gb|EKL16899.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-59A1]
 gi|408652253|gb|EKL23478.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-61A2]
 gi|408658567|gb|EKL29633.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-77A1]
 gi|408659574|gb|EKL30613.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HC-62A1]
 gi|408661979|gb|EKL32956.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HE-40]
 gi|408666146|gb|EKL36945.1| RNA polymerase sigma factor RpoD [Vibrio cholerae HE-46]
 gi|408848808|gb|EKL88845.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-37A1]
 gi|408849369|gb|EKL89390.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-17A2]
 gi|408854557|gb|EKL94310.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-02C1]
 gi|408858856|gb|EKL98526.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-46B1]
 gi|408862031|gb|EKM01583.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-55B2]
 gi|408866377|gb|EKM05760.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-44C1]
 gi|408870010|gb|EKM09292.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-59B1]
 gi|408873452|gb|EKM12649.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-62B1]
 gi|408881345|gb|EKM20241.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-69A1]
 gi|429225275|gb|EKY31542.1| RNA polymerase sigma factor RpoD [Vibrio cholerae PS15]
 gi|439975823|gb|ELP51930.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 4260B]
 gi|443432944|gb|ELS75464.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-64A1]
 gi|443436879|gb|ELS82993.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-65A1]
 gi|443440443|gb|ELS90130.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-67A1]
 gi|443444540|gb|ELS97811.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-68A1]
 gi|443448375|gb|ELT05008.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-71A1]
 gi|443451149|gb|ELT11411.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-72A2]
 gi|443455236|gb|ELT19020.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-78A1]
 gi|443458631|gb|ELT26026.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-7A1]
 gi|443462513|gb|ELT33550.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-80A1]
 gi|443466609|gb|ELT41266.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-81A1]
 gi|448266250|gb|EMB03479.1| RNA polymerase sigma factor RpoD [Vibrio cholerae O1 str. Inaba
            G4222]
          Length = 625

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
                   I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
                  I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|258623542|ref|ZP_05718543.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|258623776|ref|ZP_05718733.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|262172395|ref|ZP_06040073.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
 gi|424809496|ref|ZP_18234873.1| RNA polymerase sigma factor RpoD [Vibrio mimicus SX-4]
 gi|449146528|ref|ZP_21777301.1| RNA polymerase sigma factor RpoD [Vibrio mimicus CAIM 602]
 gi|258583899|gb|EEW08691.1| RNA polymerase sigma factor [Vibrio mimicus VM603]
 gi|258584204|gb|EEW08952.1| RNA polymerase sigma factor [Vibrio mimicus VM573]
 gi|261893471|gb|EEY39457.1| RNA polymerase sigma factor RpoD [Vibrio mimicus MB-451]
 gi|342322984|gb|EGU18770.1| RNA polymerase sigma factor RpoD [Vibrio mimicus SX-4]
 gi|449077760|gb|EMB48721.1| RNA polymerase sigma factor RpoD [Vibrio mimicus CAIM 602]
          Length = 625

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 321/629 (51%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
                   I  E S ADL+ E  E  + E                            KF+ 
Sbjct: 183  -------IGSELSEADLADEDDEVAEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRDSNQASEASSLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVREQEDDIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 314/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
                  I  E S ADL+ E  E  + E                            KF+ 
Sbjct: 183 -------IGSELSEADLADEDDEVAEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRDSNQASEASSLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVREQEDDIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|421263986|ref|ZP_15714995.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. P52VAC]
 gi|401688853|gb|EJS84396.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. P52VAC]
          Length = 622

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/623 (49%), Positives = 418/623 (67%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
              + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 409/610 (67%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
             + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|359299231|ref|ZP_09185070.1| RNA polymerase sigma factor RpoD [Haemophilus [parainfluenzae] CCUG
            13788]
 gi|402304257|ref|ZP_10823328.1| RNA polymerase sigma factor RpoD [Haemophilus sputorum HK 2154]
 gi|400378076|gb|EJP30939.1| RNA polymerase sigma factor RpoD [Haemophilus sputorum HK 2154]
          Length = 623

 Score =  573 bits (1477), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 414/611 (67%), Gaps = 13/611 (2%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + +  +LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 13   QSQIALLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVFEVAPDTDEL 72

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 73   MLAENIADEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 131

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----------N 997
            EG+ ++  A++  P  +  +L   +++ +  +++ ++V   ID N  +           +
Sbjct: 132  EGINEVQCAVAEYPEALSGVLACYEQVEEGTMRLADLVTAFIDPNLEAATEEHLDPDLHH 191

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
            +  ++G  + +EE+   ++S +  S++        +  KF+ +    +K   A +K G  
Sbjct: 192  DAEVEGAADIDEEEEDEDASDSSDSSDDNSIDPEVAREKFTKLKEQHEKALLAIQKHGRT 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +   +  + +S+     R   K  + L +T++  + QV   E+QI    V   GM +  
Sbjct: 252  HKKAREQIHALSDIFREFRLVPKQFDLLVETMQKLMKQVRAQERQIQRYAVEYAGMKKGD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K F  NE +  W++     +      L   I  I+     L  L+    L +  +R+I
Sbjct: 312  FLKAFQGNETSEEWIEKAINAKKGGAPKLANYIEKIRVNIAALQELEQSSGLTIAQIREI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
              ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 492  ELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
                ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  IATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 612  SRSETLRSFLD 622



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 405/598 (67%), Gaps = 13/598 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + +  +LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 13  QSQIALLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVFEVAPDTDEL 72

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NI  +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE
Sbjct: 73  MLAENIADEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIE 131

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----------N 207
           EG+ ++  A++  P  +  +L   +++ +  +++ ++V   ID N  +           +
Sbjct: 132 EGINEVQCAVAEYPEALSGVLACYEQVEEGTMRLADLVTAFIDPNLEAATEEHLDPDLHH 191

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
           +  ++G  + +EE+   ++S +  S++        +  KF+ +    +K   A +K G  
Sbjct: 192 DAEVEGAADIDEEEEDEDASDSSDSSDDNSIDPEVAREKFTKLKEQHEKALLAIQKHGRT 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +   +  + +S+     R   K  + L +T++  + QV   E+QI    V   GM +  
Sbjct: 252 HKKAREQIHALSDIFREFRLVPKQFDLLVETMQKLMKQVRAQERQIQRYAVEYAGMKKGD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K F  NE +  W++     +      L   I  I+     L  L+    L +  +R+I
Sbjct: 312 FLKAFQGNETSEEWIEKAINAKKGGAPKLANYIEKIRVNIAALQELEQSSGLTIAQIREI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 492 ELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 IATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|409202667|ref|ZP_11230870.1| RNA polymerase sigma factor [Pseudoalteromonas flavipulchra JG1]
          Length = 616

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/608 (51%), Positives = 408/608 (67%), Gaps = 9/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +IV G  D N    N       +   E 
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVSGFFDPNAVEENEAPISATHIGSEL 187

Query: 1012 ILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
               +    D   +  +             E+   F ++   ++  R+ FE +G +     
Sbjct: 188  SDEDLDDEDDDEDDDDDDSEEGDSGPDPEEAREHFEHLRTLYNAAREIFESKGRSHPDAK 247

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   I +     +   K  +++ + +R+ +++V   E+ I++  V    +P+  F+K F
Sbjct: 248  AAIQEIGDHFRTFKLVPKQFDRMVNNMRDMMDKVRVQERIIMKQAVQIAKVPKKVFVKHF 307

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              NE +  W+D E      ++  L    P I+    KL   +    L +  ++DINR+M 
Sbjct: 308  ANNETDTAWIDAEIASGEKHSAKLAEVKPEIERCVNKLKAFEDSTGLSIERIKDINRRMS 367

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    +
Sbjct: 488  MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRGATNE 547

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 548  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 607

Query: 1423 LKIFLEGK 1430
            LK FL+ K
Sbjct: 608  LKSFLDVK 615



 Score =  558 bits (1437), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 306/601 (50%), Positives = 401/601 (66%), Gaps = 10/601 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +IV G  D N    N       +   E 
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVSGFFDPNAVEENEAPISATHIGSEL 187

Query: 222 ILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
              +    D   +  +             E+   F ++   ++  R+ FE +G +     
Sbjct: 188 SDEDLDDEDDDEDDDDDDSEEGDSGPDPEEAREHFEHLRTLYNAAREIFESKGRSHPDAK 247

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   I +     +   K  +++ + +R+ +++V   E+ I++  V    +P+  F+K F
Sbjct: 248 AAIQEIGDHFRTFKLVPKQFDRMVNNMRDMMDKVRVQERIIMKQAVQIAKVPKKVFVKHF 307

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             NE +  W+D E      ++  L    P I+    KL   +    L +  ++DINR+M 
Sbjct: 308 ANNETDTAWIDAEIASGEKHSAKLAEVKPEIERCVNKLKAFEDSTGLSIERIKDINRRMS 367

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    +
Sbjct: 488 MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRGATNE 547

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDW 631
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D 
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 607

Query: 632 L 632
           L
Sbjct: 608 L 608


>gi|448824726|dbj|BAM78692.1| RNA polymerase sigma factor, partial [Pseudomonas cannabina pv.
           alisalensis]
 gi|448824734|dbj|BAM78696.1| RNA polymerase sigma factor, partial [Pseudomonas cannabina pv.
           alisalensis]
          Length = 584

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/592 (50%), Positives = 402/592 (67%), Gaps = 28/592 (4%)

Query: 49  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 108
           LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 1   LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 60

Query: 109 DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 168
              E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 61  AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 120

Query: 169 SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGNKNNNEEK 221
           +  P T+  IL    +++    ++ +++ G ID +               K  K   +++
Sbjct: 121 AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDE 180

Query: 222 IL-----------IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
                        +ES    +  +Q          +F  +S   +  RKA +K G + + 
Sbjct: 181 EEETAEATDDEEEVESGPDPVIAQQ----------RFGAVSDQMEITRKALKKFGRDDKH 230

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++
Sbjct: 231 AIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLR 290

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+
Sbjct: 291 QFPGHEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRR 350

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 351 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 410

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 411 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 470

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 471 ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 530

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 531 REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 582



 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 301/592 (50%), Positives = 402/592 (67%), Gaps = 28/592 (4%)

Query: 839  LGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDD 898
            LG+E+ YLT++E+ND LPEDI D E +E II+    M I V E   D + LML++  +D+
Sbjct: 1    LGREQKYLTYAEVNDHLPEDISDPEQVEDIIRMINDMGIPVHESAPDADALMLADADTDE 60

Query: 899  DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAI 958
               E   AAL+ V++D GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG+++++ AI
Sbjct: 61   AAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGIREVMGAI 120

Query: 959  SSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGNKNNNEEK 1011
            +  P T+  IL    +++    ++ +++ G ID +               K  K   +++
Sbjct: 121  AHFPGTVDHILSEYTRVTSEGGRLSDVLSGYIDPDDGIAPPAEVPPPVDPKAAKAEGDDE 180

Query: 1012 IL-----------IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
                         +ES    +  +Q          +F  +S   +  RKA +K G + + 
Sbjct: 181  EEETAEATDDEEEVESGPDPVIAQQ----------RFGAVSDQMEITRKALKKFGRDDKH 230

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I     ++   + I+   K  E L + +R  + ++   E+ I+++ V    MPR  F++
Sbjct: 231  AIAEMVALAELFMPIKLVPKQFEGLVERVRGALERLRAQERAIMQLCVRDARMPRADFLR 290

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             FP +E++ +W D   K +  Y   + R  P I+  QQKL  L+ +  L + +++DINR+
Sbjct: 291  QFPGHEVDESWTDALAKGKSKYAEAIARLQPDIQRCQQKLSALEEETGLKIAEIKDINRR 350

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 351  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 410

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  + 
Sbjct: 411  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELG 470

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M +P D A   S++   
Sbjct: 471  ERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTMQSPIDVATVESLKEAT 530

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 531  REVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 582


>gi|425066104|ref|ZP_18469224.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            gallicida P1059]
 gi|404382644|gb|EJZ79104.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            gallicida P1059]
          Length = 622

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/623 (49%), Positives = 418/623 (67%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
              + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERNIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 409/610 (67%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
             + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERNIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|254226294|ref|ZP_04919885.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
 gi|125621156|gb|EAZ49499.1| RNA polymerase sigma factor RpoD [Vibrio cholerae V51]
          Length = 625

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 419/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
                   I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G  S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRESHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 410/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
                  I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G  S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRESHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|114564160|ref|YP_751674.1| RNA polymerase sigma-70 subunit RpoD [Shewanella frigidimarina NCIMB
            400]
 gi|114335453|gb|ABI72835.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella frigidimarina
            NCIMB 400]
          Length = 614

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 307/605 (50%), Positives = 411/605 (67%), Gaps = 6/605 (0%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +
Sbjct: 9    QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 890  MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            M+S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 69   MMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 128

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKG 1003
            G+  +  ++S  P  I  IL   DK    E+++ +I+ G I+ +       ++N      
Sbjct: 129  GINTVQSSVSEYPQAIAMILEQFDKYEAEELRLSDIISGFINPDDDDVAPTATNVGSELA 188

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +  N+++    +    +           E+  KF+ +   ++K      ++G +    I 
Sbjct: 189  DSKNDDDDDDDDDDDEEEEEGNKGPDPEEAKEKFTQLREAYEKSLGIIAEKGRDHPEAIG 248

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            +   I       R   K  ++L  ++RN +++V   E+ ++++ V    MP+ +FIK F 
Sbjct: 249  SLFVIGELFKEFRLVPKQFDRLVKSMRNMMDRVRIQERLVIKLCVEHAKMPKKNFIKAFT 308

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+W + E +    Y   L      +     KL  ++ +  L +  ++DINR+M  
Sbjct: 309  GNETNLDWFNKEKESTKPYAEGLRLITDDVTRCVTKLGAIEVETDLTIAGIKDINRRMSI 368

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 369  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 429  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 488

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+++   ++
Sbjct: 489  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEV 548

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 549  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 608

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 609  KSFLD 613



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 299/592 (50%), Positives = 402/592 (67%), Gaps = 6/592 (1%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +
Sbjct: 9   QSQLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDM 68

Query: 100 MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           M+S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 69  MMSEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 128

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------FSSNNRVIKG 213
           G+  +  ++S  P  I  IL   DK    E+++ +I+ G I+ +       ++N      
Sbjct: 129 GINTVQSSVSEYPQAIAMILEQFDKYEAEELRLSDIISGFINPDDDDVAPTATNVGSELA 188

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +  N+++    +    +           E+  KF+ +   ++K      ++G +    I 
Sbjct: 189 DSKNDDDDDDDDDDDEEEEEGNKGPDPEEAKEKFTQLREAYEKSLGIIAEKGRDHPEAIG 248

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           +   I       R   K  ++L  ++RN +++V   E+ ++++ V    MP+ +FIK F 
Sbjct: 249 SLFVIGELFKEFRLVPKQFDRLVKSMRNMMDRVRIQERLVIKLCVEHAKMPKKNFIKAFT 308

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+W + E +    Y   L      +     KL  ++ +  L +  ++DINR+M  
Sbjct: 309 GNETNLDWFNKEKESTKPYAEGLRLITDDVTRCVTKLGAIEVETDLTIAGIKDINRRMSI 368

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 369 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 428

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 429 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 488

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S+++   ++
Sbjct: 489 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKNATHEV 548

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|417854029|ref|ZP_12499357.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. Anand1_goat]
 gi|338218661|gb|EGP04418.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. Anand1_goat]
          Length = 622

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/623 (49%), Positives = 417/623 (66%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
                +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFAEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 408/610 (66%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
               +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFAEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|410613855|ref|ZP_11324908.1| RNA polymerase primary sigma factor [Glaciecola psychrophila 170]
 gi|410166572|dbj|GAC38797.1| RNA polymerase primary sigma factor [Glaciecola psychrophila 170]
          Length = 607

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 306/618 (49%), Positives = 419/618 (67%), Gaps = 28/618 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 2    VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQMEDIIRMINDMGIKVFERAPD 61

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             + L++ +  +DD+  EA  AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62   KDELLMQDNDTDDEAAEAAAAALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 1002
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N    +     + 
Sbjct: 122  RIEEGINQVQCSVAEYPEAITHLLDQWDMFEAEEIRLSDIIIGFVDPNEQDVAPTATHVG 181

Query: 1003 GNKNNNEEKILIESSSADLS--TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
               ++ E K        +    T    +L  E   KF+ +   ++K R   + +G + + 
Sbjct: 182  SELSSKELKEEDGDDEEEEEEDTGPDPELARE---KFTALRHQYEKARDVIDAKGRSHKE 238

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
                 N +S      R T K  +++   +R+ ++++   E+ +++  V    MP+  FIK
Sbjct: 239  ARVQINELSEVFKEFRLTPKQFDRMVKNMRSMMDRIRVQERIVMKHCVITAKMPKKDFIK 298

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQTDIVLP 1170
             F  NE +  W+            IL  ++P  +E+++          K+  ++ +  L 
Sbjct: 299  AFSGNETSTVWLFK----------ILNSSLPYAEEMREHQEELERAISKMNTVEDETGLI 348

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 349  IADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 408

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 409  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 468

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI+D+ +  P D+
Sbjct: 469  GREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIQDDTITQPLDS 528

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 529  ATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 588

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR  +LK FL+
Sbjct: 589  LRKLRHPSRSEQLKSFLD 606



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 298/605 (49%), Positives = 409/605 (67%), Gaps = 28/605 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 2   VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQMEDIIRMINDMGIKVFERAPD 61

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            + L++ +  +DD+  EA  AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62  KDELLMQDNDTDDEAAEAAAAALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 212
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N    +     + 
Sbjct: 122 RIEEGINQVQCSVAEYPEAITHLLDQWDMFEAEEIRLSDIIIGFVDPNEQDVAPTATHVG 181

Query: 213 GNKNNNEEKILIESSSADLS--TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
              ++ E K        +    T    +L  E   KF+ +   ++K R   + +G + + 
Sbjct: 182 SELSSKELKEEDGDDEEEEEEDTGPDPELARE---KFTALRHQYEKARDVIDAKGRSHKE 238

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
                N +S      R T K  +++   +R+ ++++   E+ +++  V    MP+  FIK
Sbjct: 239 ARVQINELSEVFKEFRLTPKQFDRMVKNMRSMMDRIRVQERIVMKHCVITAKMPKKDFIK 298

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLINLQTDIVLP 380
            F  NE +  W+            IL  ++P  +E+++          K+  ++ +  L 
Sbjct: 299 AFSGNETSTVWLFK----------ILNSSLPYAEEMREHQEELERAISKMNTVEDETGLI 348

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 349 IADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 408

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 409 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 468

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI+D+ +  P D+
Sbjct: 469 GREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIQDDTITQPLDS 528

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 529 ATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 588

Query: 621 LRKLR 625
           LRKLR
Sbjct: 589 LRKLR 593


>gi|392542214|ref|ZP_10289351.1| RNA polymerase sigma factor [Pseudoalteromonas piscicida JCM 20779]
          Length = 616

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 313/608 (51%), Positives = 409/608 (67%), Gaps = 9/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVSENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-FSSNNRVIKGNKNNNEE 1010
              +  +++  P  I  +L   DK    E+++ +IV G  D N    +   I      +E 
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVSGFFDPNAIEEDEAPISATHIGSEL 187

Query: 1011 KILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
                     D   +  +  +         E+   F  +   ++K R+ FE +G +     
Sbjct: 188  SDEDLDDEDDDEDDDDDDSEEGDSGPDPEEAREHFEQLRTLYNKAREIFESKGRSHPDAK 247

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   I +     +   K  +++ + +R+ +++V   E+ I++  V    +P+  F+K F
Sbjct: 248  AAIQEIGDHFRTFKLVPKQFDRMVNNMRDMMDKVRVQERIIMKQAVQIAKVPKKVFVKHF 307

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              NE +  W+D E      ++  L    P I+    KL   +    L +  ++DINR+M 
Sbjct: 308  ANNETDTAWIDAEIASGEKHSAKLAEVKPEIERCVNKLKAFEDSTGLSIERIKDINRRMS 367

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    +
Sbjct: 488  MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRGATNE 547

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 548  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 607

Query: 1423 LKIFLEGK 1430
            LK FL+ K
Sbjct: 608  LKSFLDVK 615



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/601 (51%), Positives = 402/601 (66%), Gaps = 10/601 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I VSE+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVSENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIQIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-FSSNNRVIKGNKNNNEE 220
             +  +++  P  I  +L   DK    E+++ +IV G  D N    +   I      +E 
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVSGFFDPNAIEEDEAPISATHIGSEL 187

Query: 221 KILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
                    D   +  +  +         E+   F  +   ++K R+ FE +G +     
Sbjct: 188 SDEDLDDEDDDEDDDDDDSEEGDSGPDPEEAREHFEQLRTLYNKAREIFESKGRSHPDAK 247

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   I +     +   K  +++ + +R+ +++V   E+ I++  V    +P+  F+K F
Sbjct: 248 AAIQEIGDHFRTFKLVPKQFDRMVNNMRDMMDKVRVQERIIMKQAVQIAKVPKKVFVKHF 307

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             NE +  W+D E      ++  L    P I+    KL   +    L +  ++DINR+M 
Sbjct: 308 ANNETDTAWIDAEIASGEKHSAKLAEVKPEIERCVNKLKAFEDSTGLSIERIKDINRRMS 367

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 487

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    +
Sbjct: 488 MMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPIDSATMESLRGATNE 547

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDW 631
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D 
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 607

Query: 632 L 632
           L
Sbjct: 608 L 608


>gi|378775713|ref|YP_005177956.1| RNA polymerase sigma factor RpoD [Pasteurella multocida 36950]
 gi|356598261|gb|AET16987.1| RNA polymerase sigma factor RpoD [Pasteurella multocida 36950]
          Length = 622

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 309/623 (49%), Positives = 418/623 (67%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
              + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLAPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   ++     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEMRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 409/610 (67%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
             + +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFDEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLAPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   ++     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEMRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|120599857|ref|YP_964431.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146292207|ref|YP_001182631.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
            CN-32]
 gi|120559950|gb|ABM25877.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. W3-18-1]
 gi|145563897|gb|ABP74832.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
            CN-32]
          Length = 616

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 308/605 (50%), Positives = 412/605 (68%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 131  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 190

Query: 1010 EKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +    +    D      E          E+  +FS +   ++   K  E +G      +K
Sbjct: 191  DLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIEAKGREHPESVK 250

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       R   K  ++L  ++R+ +++V   E+  +++ V +  MP+ +F+K F 
Sbjct: 251  ALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFT 310

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+W   E      Y   L      +   + KL  ++ +  L ++ ++DINR+M  
Sbjct: 311  GNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSI 370

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 431  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 490

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   ++
Sbjct: 491  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEV 550

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 551  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 610

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 611  KSFLD 615



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 300/592 (50%), Positives = 403/592 (68%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 131 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 190

Query: 220 EKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +    +    D      E          E+  +FS +   ++   K  E +G      +K
Sbjct: 191 DLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIEAKGREHPESVK 250

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       R   K  ++L  ++R+ +++V   E+  +++ V +  MP+ +F+K F 
Sbjct: 251 ALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFT 310

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+W   E      Y   L      +   + KL  ++ +  L ++ ++DINR+M  
Sbjct: 311 GNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSI 370

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 490

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   ++
Sbjct: 491 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEV 550

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|422909039|ref|ZP_16943691.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-09]
 gi|424658392|ref|ZP_18095649.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-16]
 gi|341636121|gb|EGS60824.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-09]
 gi|408055114|gb|EKG90057.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-16]
          Length = 625

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 419/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 175

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
            +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 176  EAPTATHIGSELSEADLADEDDAVVEDEEEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A   + +     R T K  + L +TLR  +++V   
Sbjct: 236  LRGKFQNLQLAVNEFGRDSNQASEASGLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  RERIRQIEAKALRKLRHPSRSEVLRSFLD 624



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 410/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 175

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
           +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 176 EAPTATHIGSELSEADLADEDDAVVEDEEEDEDEDGDGESSDSEEEVGIDPELAREKFNE 235

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A   + +     R T K  + L +TLR  +++V   
Sbjct: 236 LRGKFQNLQLAVNEFGRDSNQASEASGLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 295

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 296 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 355

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 475

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 476 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 535

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 536 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 595

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 596 RERIRQIEAKALRKLR 611


>gi|261868195|ref|YP_003256117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans D11S-1]
 gi|415770838|ref|ZP_11485084.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans D17P-2]
 gi|444345851|ref|ZP_21153855.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype c str. AAS4A]
 gi|261413527|gb|ACX82898.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
            actinomycetemcomitans D11S-1]
 gi|348656619|gb|EGY74229.1| RNA polymerase sigma factor RpoD [Aggregatibacter
            actinomycetemcomitans D17P-2]
 gi|443542392|gb|ELT52729.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
            actinomycetemcomitans serotype c str. AAS4A]
          Length = 616

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 414/614 (67%), Gaps = 13/614 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIVQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +      +
Sbjct: 122  RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEGLAE 181

Query: 1006 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 1054
            + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182  DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242  GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302  KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362  REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482  SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542  SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 602  RHPSRSETLRSFLD 615



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 298/601 (49%), Positives = 405/601 (67%), Gaps = 13/601 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIVQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+ NIT +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNENITDEDVVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  AI++ P  I  ++   D +    +++ +++ G +D N  + +      +
Sbjct: 122 RIEEGINEVQSAIAAYPEAITYLIEQYDLVENGGVRLADLITGFVDPNVLTESETEGLAE 181

Query: 216 N-NNEEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKE 264
           + N+EE   I+S S +    +                    KF+ +     K  ++  K 
Sbjct: 182 DFNSEEGGDIDSESEEEEDNEGGSSDDSDSDNSVDPEIAREKFTALKQQHQKTLESIAKH 241

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  ++        +S+     R   K  + L  ++R  + +V   E+ I  IVV+   MP
Sbjct: 242 GRTAKKAKDEIQVLSDIFTQFRLVPKQFDMLVLSIRGIMKRVRGQERFIQRIVVDNAKMP 301

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  F K F  +E    W+         ++  L +    +++    L+ ++ D  L +  +
Sbjct: 302 KSGFQKSFIGHETTDTWLVKALSAGKSWSEKLVQYENQLRQAITNLVQIEQDTHLTIPQI 361

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 362 REIGERITQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 421

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E 
Sbjct: 422 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREA 481

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   
Sbjct: 482 SPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATVQ 541

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 542 SLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601

Query: 625 R 625
           R
Sbjct: 602 R 602


>gi|117921525|ref|YP_870717.1| RNA polymerase sigma-70 subunit RpoD [Shewanella sp. ANA-3]
 gi|117613857|gb|ABK49311.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella sp. ANA-3]
          Length = 619

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/608 (50%), Positives = 410/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 1008
              +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131  NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 1009 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +     +    +      E            E+  +FS +   ++   K  + +G     
Sbjct: 191  DLDDEDDDEDDEDEDGDGEGDDDGNKGPDPEEARERFSQLRTAYENALKIIDAKGREHPE 250

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I+A   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251  SIQALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311  FFTGNETNLDWFDAEKNSTKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 551  HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 610

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 611  EILKSFLD 618



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 401/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 218
             +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 131 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 190

Query: 219 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +     +    +      E            E+  +FS +   ++   K  + +G     
Sbjct: 191 DLDDEDDDEDDEDEDGDGEGDDDGNKGPDPEEARERFSQLRTAYENALKIIDAKGREHPE 250

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I+A   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 251 SIQALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 310

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  NE NL+W D E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 311 FFTGNETNLDWFDAEKNSTKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 370

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 371 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 430

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 490

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 491 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 550

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|421350352|ref|ZP_15800718.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-25]
 gi|395954474|gb|EJH65084.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HE-25]
          Length = 627

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/631 (50%), Positives = 420/631 (66%), Gaps = 36/631 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------------KF 1037
                   I  E S ADL+ E    ++ E                              KF
Sbjct: 183  -------IGSELSEADLADEDDAVVEDEDEDEDEDEDGDGESSDSEEEVGIDPELAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V 
Sbjct: 236  NELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 295

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
              E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   
Sbjct: 296  TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSI 355

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 356  QKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 415

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 416  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 475

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 476  KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 535

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 536  FIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 595

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 626



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/618 (50%), Positives = 411/618 (66%), Gaps = 36/618 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------------KF 247
                  I  E S ADL+ E    ++ E                              KF
Sbjct: 183 -------IGSELSEADLADEDDAVVEDEDEDEDEDEDGDGESSDSEEEVGIDPELAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           + +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V 
Sbjct: 236 NELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 295

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
             E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   
Sbjct: 296 TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSI 355

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 356 QKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 415

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 416 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 475

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 476 KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 535

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 536 FIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 595

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 596 VTRERIRQIEAKALRKLR 613


>gi|388600384|ref|ZP_10158780.1| RNA polymerase sigma factor RpoD [Vibrio campbellii DS40M4]
          Length = 620

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 314/622 (50%), Positives = 417/622 (67%), Gaps = 25/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 1046
                +E   L ES   +   E ++  +                   +L KF+ +   +  
Sbjct: 181  THIGSE---LTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 237

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238  LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298  AVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358  TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538  PLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 598  EAKALRKLRHPSRSETLRSFLD 619



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/609 (50%), Positives = 408/609 (66%), Gaps = 25/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 256
               +E   L ES   +   E ++  +                   +L KF+ +   +  
Sbjct: 181 THIGSE---LTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 237

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238 LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298 AVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358 TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538 PLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 598 EAKALRKLR 606


>gi|257464575|ref|ZP_05628946.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
 gi|257450235|gb|EEV24278.1| RNA polymerase sigma factor RpoD [Actinobacillus minor 202]
          Length = 621

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 405/610 (66%), Gaps = 12/610 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12   QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72   MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
            EG+ ++  A++  P  ++ +L    ++   E+++ +++   +D N      + +    ++
Sbjct: 131  EGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLITAFVDPNAQEETPIDEDAHLDD 190

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNS 1058
            EE  ++     +   E  +                  KF+ +    +K   A +K G   
Sbjct: 191  EESDIVADVDDESEDEDGDSSSDNGDDSSIDPELAREKFAALKAQHEKALLAIQKHGRTH 250

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                +  N +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F
Sbjct: 251  AKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADF 310

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +K F  NE    W++     +      L   +  I+     L NL+    L +  +R+I 
Sbjct: 311  LKAFQNNETTEAWIEKAINAKKGGAPKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIG 370

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371  GRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 431  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 490

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 491  LAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 550

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 551  ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 611  RSETLRSFLD 620



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 396/597 (66%), Gaps = 12/597 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12  QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72  MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
           EG+ ++  A++  P  ++ +L    ++   E+++ +++   +D N      + +    ++
Sbjct: 131 EGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLITAFVDPNAQEETPIDEDAHLDD 190

Query: 219 EEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNS 268
           EE  ++     +   E  +                  KF+ +    +K   A +K G   
Sbjct: 191 EESDIVADVDDESEDEDGDSSSDNGDDSSIDPELAREKFAALKAQHEKALLAIQKHGRTH 250

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
               +  N +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F
Sbjct: 251 AKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADF 310

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           +K F  NE    W++     +      L   +  I+     L NL+    L +  +R+I 
Sbjct: 311 LKAFQNNETTEAWIEKAINAKKGGAPKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIG 370

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
            ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371 GRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 431 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 490

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 491 LAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 550

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 607


>gi|329898803|ref|ZP_08272472.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
 gi|328920738|gb|EGG28203.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC3088]
          Length = 600

 Score =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 412/599 (68%), Gaps = 11/599 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V E   D + L++
Sbjct: 10   RLKSLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEEAPDADELLM 69

Query: 892  S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            +  + ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TEGDSSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            G+++++ A++  P  +  +L    ++++ E ++ +++ G +D      + V    +    
Sbjct: 130  GIRELMAALAHYPGAVEHVLNEYAQVTQEERRLGDVMVGYLD----PADEVPTAAEVAAA 185

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 1069
             +   +    D   + +E  K     +F  +   ++K  KA  ++G  S+  +K  + + 
Sbjct: 186  NEASGDDEEGDSGPDPVEAAK-----RFKELRKQWEKTEKALAEKGRQSKVTLKELDKLG 240

Query: 1070 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 1129
                  + T +  + L D  R+ + +V   E++I+ I V  C +PR  FI  F  NE N 
Sbjct: 241  EVFKFFKLTPRVFDPLLDMARDVLQEVRTQEREIMTICVRHCSVPRKAFIDSFVGNETNE 300

Query: 1130 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 1189
             W+D+  K   +    L  +  ++  LQ+++I  +    L ++++++INR+M  GE +AR
Sbjct: 301  AWLDDLIKKAPERAAKLEADRDTLMRLQRRIIATEEKSGLSVSEIKEINRRMSMGEARAR 360

Query: 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249
            +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 361  RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 420

Query: 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 1309
            WIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+MPE+K
Sbjct: 421  WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDK 480

Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
            +RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    ++    ++L  LT 
Sbjct: 481  VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTIASPVDSATGQGLQEATTEVLAGLTA 540

Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL+
Sbjct: 541  REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 599



 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/594 (49%), Positives = 407/594 (68%), Gaps = 12/594 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V E   D + L++
Sbjct: 10  RLKSLIAKGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIQVFEEAPDADELLM 69

Query: 102 S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           +  + ++DD       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TEGDSSADDIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           G+++++ A++  P  +  +L    ++++ E ++ +++ G +D      + V    +    
Sbjct: 130 GIRELMAALAHYPGAVEHVLNEYAQVTQEERRLGDVMVGYLD----PADEVPTAAEVAAA 185

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 279
            +   +    D   + +E  K     +F  +   ++K  KA  ++G  S+  +K  + + 
Sbjct: 186 NEASGDDEEGDSGPDPVEAAK-----RFKELRKQWEKTEKALAEKGRQSKVTLKELDKLG 240

Query: 280 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 339
                 + T +  + L D  R+ + +V   E++I+ I V  C +PR  FI  F  NE N 
Sbjct: 241 EVFKFFKLTPRVFDPLLDMARDVLQEVRTQEREIMTICVRHCSVPRKAFIDSFVGNETNE 300

Query: 340 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 399
            W+D+  K   +    L  +  ++  LQ+++I  +    L ++++++INR+M  GE +AR
Sbjct: 301 AWLDDLIKKAPERAAKLEADRDTLMRLQRRIIATEEKSGLSVSEIKEINRRMSMGEARAR 360

Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
           +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 361 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 420

Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
           WIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+MPE+K
Sbjct: 421 WIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDK 480

Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
           +RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    ++    ++L  LT 
Sbjct: 481 VRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTIASPVDSATGQGLQEATTEVLAGLTA 540

Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D+L
Sbjct: 541 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYL 594


>gi|383311804|ref|YP_005364614.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. HN06]
 gi|386835757|ref|YP_006241077.1| protein RpoD [Pasteurella multocida subsp. multocida str. 3480]
 gi|380873076|gb|AFF25443.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            multocida str. HN06]
 gi|385202463|gb|AFI47318.1| RpoD [Pasteurella multocida subsp. multocida str. 3480]
          Length = 622

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/623 (49%), Positives = 417/623 (66%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
                +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFAEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKVKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 408/610 (66%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
               +E+    +S SA L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFAEDEDS---DSVSATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKVKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|375264393|ref|YP_005021836.1| RNA polymerase sigma factor RpoD [Vibrio sp. EJY3]
 gi|369839717|gb|AEX20861.1| RNA polymerase sigma factor RpoD [Vibrio sp. EJY3]
          Length = 623

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 313/621 (50%), Positives = 417/621 (67%), Gaps = 20/621 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDAEDTAAPTAT 181

Query: 1004 NKNN--NEEKILIESSSADLSTEQLEKLKYE--------------SLIKFSNISFHFDKM 1047
            +  +  +E ++  E  +     ++ E    +              +L KF+ +   +  +
Sbjct: 182  HIGSELSESQLEDEDDTDVDDDDEDEDGDDDSEDTEEDVGIDPELALEKFNQLRSTYQNL 241

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
            + A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 242  QLAINEYGYESPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSV 301

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 302  VEYGKMPKKSFIALFTGNESSDAWLDEILASDKPYAEKIKRNEEEIRRSITKLKMIEEET 361

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 362  SLSVQNVKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 421

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 422  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 481

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 482  QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 541

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 542  LDSATATSLKGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 601

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 602  AKALRKLRHPSRSETLRSFLD 622



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 306/608 (50%), Positives = 408/608 (67%), Gaps = 20/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKSLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDAEDTAAPTAT 181

Query: 214 NKNN--NEEKILIESSSADLSTEQLEKLKYE--------------SLIKFSNISFHFDKM 257
           +  +  +E ++  E  +     ++ E    +              +L KF+ +   +  +
Sbjct: 182 HIGSELSESQLEDEDDTDVDDDDEDEDGDDDSEDTEEDVGIDPELALEKFNQLRSTYQNL 241

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
           + A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ V
Sbjct: 242 QLAINEYGYESPKATVANEMMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSV 301

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ + 
Sbjct: 302 VEYGKMPKKSFIALFTGNESSDAWLDEILASDKPYAEKIKRNEEEIRRSITKLKMIEEET 361

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 362 SLSVQNVKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 421

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 422 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 481

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P
Sbjct: 482 QEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELP 541

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 542 LDSATATSLKGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 601

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 602 AKALRKLR 609


>gi|386312882|ref|YP_006009047.1| RNA polymerase sigma-70 subunit RpoD [Shewanella putrefaciens 200]
 gi|319425507|gb|ADV53581.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens 200]
          Length = 613

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 308/605 (50%), Positives = 412/605 (68%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 128  NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 187

Query: 1010 EKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +    +    D      E          E+  +FS +   ++   K  E +G      +K
Sbjct: 188  DLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIEAKGREHPESVK 247

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       R   K  ++L  ++R+ +++V   E+  +++ V +  MP+ +F+K F 
Sbjct: 248  ALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFT 307

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE NL+W   E      Y   L      +   + KL  ++ +  L ++ ++DINR+M  
Sbjct: 308  GNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSI 367

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 428  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 487

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   ++
Sbjct: 488  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEV 547

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 548  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 607

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 608  KSFLD 612



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 300/592 (50%), Positives = 403/592 (68%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI--DKNFSSNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+   +E+++ +I+ G +  D+   +      G++ ++E
Sbjct: 128 NTVQSSVAEYPQAIAMILEQFDQFEADELRLSDIISGFVNPDEEDVAPTATHIGSELSDE 187

Query: 220 EKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +    +    D      E          E+  +FS +   ++   K  E +G      +K
Sbjct: 188 DLDDEDDEDEDDEDADEEDDANKGPDPEEARERFSQLRAAYENALKIIEAKGREHPESVK 247

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       R   K  ++L  ++R+ +++V   E+  +++ V +  MP+ +F+K F 
Sbjct: 248 ALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLAMKLCVEQAKMPKKNFVKFFT 307

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE NL+W   E      Y   L      +   + KL  ++ +  L ++ ++DINR+M  
Sbjct: 308 GNETNLDWFHAEKASNKPYAEGLRMVEEDVLRCRSKLAAVEEETGLAISAIKDINRRMSI 367

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 368 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 487

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S   ++
Sbjct: 488 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSATHEV 547

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|156973168|ref|YP_001444075.1| RNA polymerase sigma factor RpoD [Vibrio harveyi ATCC BAA-1116]
 gi|444424659|ref|ZP_21220114.1| RNA polymerase sigma factor RpoD [Vibrio campbellii CAIM 519 = NBRC
            15631]
 gi|156524762|gb|ABU69848.1| hypothetical protein VIBHAR_00848 [Vibrio harveyi ATCC BAA-1116]
 gi|444242151|gb|ELU53667.1| RNA polymerase sigma factor RpoD [Vibrio campbellii CAIM 519 = NBRC
            15631]
          Length = 620

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 314/622 (50%), Positives = 417/622 (67%), Gaps = 25/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 1046
                +E   L ES   +   E ++  +                   +L KF+ +   +  
Sbjct: 181  THIGSE---LTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 237

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238  LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298  AVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358  TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538  PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 598  EAKALRKLRHPSRSETLRSFLD 619



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/609 (50%), Positives = 408/609 (66%), Gaps = 25/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 256
               +E   L ES   +   E ++  +                   +L KF+ +   +  
Sbjct: 181 THIGSE---LTESQLEEEDEEDVDDDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 237

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238 LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298 AVEYGKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358 TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538 PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 598 EAKALRKLR 606


>gi|410633994|ref|ZP_11344634.1| RNA polymerase primary sigma factor [Glaciecola arctica BSs20135]
 gi|410146654|dbj|GAC21501.1| RNA polymerase primary sigma factor [Glaciecola arctica BSs20135]
          Length = 608

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/627 (48%), Positives = 413/627 (65%), Gaps = 45/627 (7%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 2    VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQMEDIIRMINDMGIKVFETAPD 61

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             + L++    +DD+  EA   ALSTV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62   KDELLMQESDTDDEAAEAAAQALSTVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------ 993
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N            
Sbjct: 122  RIEEGINQVQCSVAEYPEAITHLLDQWDLFEAEEIRLSDIIIGFVDPNEQDVAPTATHVG 181

Query: 994  --FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
               S      +   ++ +E+        +L+ E           KF+ +   ++K R   
Sbjct: 182  SELSKEELAEEDGDDDEDEEEEDTGPDPELARE-----------KFTALRIQYEKARDVI 230

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
              +G + +        +S      R T K  +++   +R+ +N++   E+ +++  V   
Sbjct: 231  NAKGRSHKEARVQIFELSEVFKEFRLTPKQFDRMVKNMRSMMNRIRVQERIVMKHCVETA 290

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLI 1161
             MP+  FIK F  NE +  W+            IL   +P  +E++           K+ 
Sbjct: 291  KMPKKDFIKAFAGNETSTVWLFK----------ILDSALPYAEEMRGHQEELERAIGKMN 340

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++ +  L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 341  AVEEETGLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 400

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 401  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 460

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQ+LQE G EP P  ++ +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 461  ISRQMLQEMGREPTPEELSERMLMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIED 520

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
              ++ P D+A   S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 521  STIVQPLDSATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 580

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR  +LK FL+
Sbjct: 581  RIRQIEAKALRKLRHPSRSEQLKSFLD 607



 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 297/614 (48%), Positives = 403/614 (65%), Gaps = 45/614 (7%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 2   VQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQMEDIIRMINDMGIKVFETAPD 61

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            + L++    +DD+  EA   ALSTV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 62  KDELLMQESDTDDEAAEAAAQALSTVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN------------ 203
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N            
Sbjct: 122 RIEEGINQVQCSVAEYPEAITHLLDQWDLFEAEEIRLSDIIIGFVDPNEQDVAPTATHVG 181

Query: 204 --FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
              S      +   ++ +E+        +L+ E           KF+ +   ++K R   
Sbjct: 182 SELSKEELAEEDGDDDEDEEEEDTGPDPELARE-----------KFTALRIQYEKARDVI 230

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
             +G + +        +S      R T K  +++   +R+ +N++   E+ +++  V   
Sbjct: 231 NAKGRSHKEARVQIFELSEVFKEFRLTPKQFDRMVKNMRSMMNRIRVQERIVMKHCVETA 290

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ----------KLI 371
            MP+  FIK F  NE +  W+            IL   +P  +E++           K+ 
Sbjct: 291 KMPKKDFIKAFAGNETSTVWLFK----------ILDSALPYAEEMRGHQEELERAIGKMN 340

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            ++ +  L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 341 AVEEETGLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 400

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 401 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 460

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           ISRQ+LQE G EP P  ++ +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 461 ISRQMLQEMGREPTPEELSERMLMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIED 520

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
             ++ P D+A   S++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 521 STIVQPLDSATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 580

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 581 RIRQIEAKALRKLR 594


>gi|229507128|ref|ZP_04396634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229509009|ref|ZP_04398497.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229512571|ref|ZP_04402042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229519677|ref|ZP_04409120.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229520813|ref|ZP_04410235.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229530331|ref|ZP_04419719.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229606193|ref|YP_002876841.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
 gi|229332104|gb|EEN97592.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 12129(1)]
 gi|229342046|gb|EEO07042.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TM 11079-80]
 gi|229344366|gb|EEO09341.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC9]
 gi|229350464|gb|EEO15413.1| RNA polymerase sigma factor RpoD [Vibrio cholerae TMA 21]
 gi|229353934|gb|EEO18868.1| RNA polymerase sigma factor RpoD [Vibrio cholerae B33]
 gi|229355873|gb|EEO20793.1| RNA polymerase sigma factor RpoD [Vibrio cholerae BX 330286]
 gi|229368848|gb|ACQ59271.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MJ-1236]
          Length = 642

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 20   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 79

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 80   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 139

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 140  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 192

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
            +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 193  EAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 252

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 253  LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 312

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 313  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 372

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 373  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 433  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 492

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 493  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 552

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 553  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 612

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 613  RERIRQIEAKALRKLRHPSRSEVLRSFLD 641



 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 20  QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 79

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 80  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 139

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 140 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 192

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
           +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 193 EAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 252

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 253 LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 312

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 313 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQK 372

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 373 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 433 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 492

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 493 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 552

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 553 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 612

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 613 RERIRQIEAKALRKLR 628


>gi|424031951|ref|ZP_17771373.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HENC-01]
 gi|408876513|gb|EKM15627.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HENC-01]
          Length = 620

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 314/622 (50%), Positives = 418/622 (67%), Gaps = 25/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 1046
                +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 181  THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPELALEKFNQLRSTYQN 237

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238  LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298  AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358  TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538  PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 598  EAKALRKLRHPSRSETLRSFLD 619



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/609 (50%), Positives = 409/609 (67%), Gaps = 25/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 180

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 256
               +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 181 THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDTEEDVGIDPELALEKFNQLRSTYQN 237

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238 LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKS 297

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + RN   I+    KL  ++ +
Sbjct: 298 AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRNEEEIRRSIAKLKMIEEE 357

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358 TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538 PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 598 EAKALRKLR 606


>gi|229525180|ref|ZP_04414585.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis VL426]
 gi|229338761|gb|EEO03778.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis VL426]
          Length = 642

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 319/629 (50%), Positives = 420/629 (66%), Gaps = 34/629 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 20   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 79

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 80   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 139

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 140  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 192

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 1039
            +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 193  EAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 252

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 1099
            +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 253  LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 312

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 1159
            E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 313  ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVRAQQEEIRRSIQK 372

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 373  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 433  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 492

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
            +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 493  NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 552

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 553  EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 612

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 613  RERIRQIEAKALRKLRHPSRSEVLRSFLD 641



 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 312/616 (50%), Positives = 411/616 (66%), Gaps = 34/616 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 20  QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 79

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 80  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 139

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 140 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 192

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------------KFSN 249
           +      I  E S ADL+ E    ++ E                            KF+ 
Sbjct: 193 EAPTATHIGSELSEADLADEDDAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNE 252

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQI 309
           +   F  ++ A  + G +S    +A + + +     R T K  + L +TLR  +++V   
Sbjct: 253 LRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQ 312

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQK 369
           E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   QK
Sbjct: 313 ERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVRAQQEEIRRSIQK 372

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           L  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 373 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 433 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 492

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
           +RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFI
Sbjct: 493 NRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFI 552

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVT
Sbjct: 553 EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 612

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKLR
Sbjct: 613 RERIRQIEAKALRKLR 628


>gi|92113104|ref|YP_573032.1| sigma 70 (RpoD) [Chromohalobacter salexigens DSM 3043]
 gi|91796194|gb|ABE58333.1| RNA polymerase, sigma 70 subunit, RpoD [Chromohalobacter salexigens
            DSM 3043]
          Length = 614

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 308/610 (50%), Positives = 409/610 (67%), Gaps = 18/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+G+LT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 9    RLKELIAQGKEQGFLTYAEVNDHLPEDIADPDQVEDIIAMINDMGISVVEEAPDEDTLMM 68

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 69   SDQSADESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 128

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ +++  P  +  IL A D     E   ++ ++  G ID +       I G      
Sbjct: 129  REVMSSLAYLPGAVDSILSAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEAEV 183

Query: 1010 EKILIESSSADLSTEQLEKLKY-----------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             +   E S+AD    + +               E+  +F  I    ++ + A E+ G  S
Sbjct: 184  PEPEPEPSAADGDVSEDDDEAEEEETGGGPDPEEARARFEQIREQNERAKAAIEEHGLGS 243

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +        ++     I+   K  E+L   +R  + Q+   EK I++I V +  +PR  F
Sbjct: 244  KEASAEQARLAELFSPIKLVPKHFERLVGQVRISVEQIRGQEKAIMQIFVKQAKVPRKTF 303

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I  FP  E +L W+D        +   L      I+  Q+K+   +  ++LP++ ++++N
Sbjct: 304  IGSFPGAESDLEWLDRFMAKHTKFADRLEPFRADIQRAQRKIGFEEEMVLLPVSHIKEVN 363

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 364  RRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 423

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 424  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 483

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D+A    +  
Sbjct: 484  LGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDSATGEGLIE 543

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 544  ATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 603

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 604  RSEPLRTFLD 613



 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 301/597 (50%), Positives = 400/597 (67%), Gaps = 18/597 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+G+LT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 9   RLKELIAQGKEQGFLTYAEVNDHLPEDIADPDQVEDIIAMINDMGISVVEEAPDEDTLMM 68

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 69  SDQSADESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 128

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ +++  P  +  IL A D     E   ++ ++  G ID +       I G      
Sbjct: 129 REVMSSLAYLPGAVDSILSAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEAEV 183

Query: 220 EKILIESSSADLSTEQLEKLKY-----------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
            +   E S+AD    + +               E+  +F  I    ++ + A E+ G  S
Sbjct: 184 PEPEPEPSAADGDVSEDDDEAEEEETGGGPDPEEARARFEQIREQNERAKAAIEEHGLGS 243

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +        ++     I+   K  E+L   +R  + Q+   EK I++I V +  +PR  F
Sbjct: 244 KEASAEQARLAELFSPIKLVPKHFERLVGQVRISVEQIRGQEKAIMQIFVKQAKVPRKTF 303

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I  FP  E +L W+D        +   L      I+  Q+K+   +  ++LP++ ++++N
Sbjct: 304 IGSFPGAESDLEWLDRFMAKHTKFADRLEPFRADIQRAQRKIGFEEEMVLLPVSHIKEVN 363

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 364 RRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 423

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 424 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 483

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  ML P D+A    +  
Sbjct: 484 LGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDGTMLLPIDSATGEGLIE 543

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 ATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|387769884|ref|ZP_10126078.1| RNA polymerase sigma factor RpoD [Pasteurella bettyae CCUG 2042]
 gi|386905640|gb|EIJ70399.1| RNA polymerase sigma factor RpoD [Pasteurella bettyae CCUG 2042]
          Length = 618

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 300/626 (47%), Positives = 421/626 (67%), Gaps = 37/626 (5%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V +   D +
Sbjct: 4    NPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLDSAPDAD 63

Query: 888  TLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
             LML+ NI  +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKR
Sbjct: 64   DLMLNENIADEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+ ++  A++  P  +  ++   +++    +++ +I+ G +D N  +    +   ++
Sbjct: 123  IEDGINEVQSAVAEYPEALAYLIEQYEQVEDGSVRLADIITGFVDPNAIAEEEHLSELED 182

Query: 1007 NNEEKILIESSS------------------------ADLSTEQLEKLKYESLIKFSNISF 1042
               E+  +++ +                         +++ E+   LK +     + I+ 
Sbjct: 183  ELSEEAEVDTDALDDEDDEESDDSDSSSDDGDNSIDPEVAREKFTALKEQCEKTLATIAK 242

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
            H         + G  S+  I+A ++I  +    R   +  + L  ++R+ + +V   E+Q
Sbjct: 243  HG--------RTGKKSKEQIQALSDIFTQF---RLVPRQFDTLVLSMRSIMKRVRTEERQ 291

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            I  + V+   MP+ +F+K F   E +  W+D     +  +   L +  P I+    +L  
Sbjct: 292  IQRLAVDYAKMPKEYFLKAFIGKENSEAWLDKLLDGKKPFVEKLQQRAPDIRISIGRLQQ 351

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            ++ D  L +  +RDI  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 352  IEQDTNLTVQQIRDIGERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 411

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 412  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 471

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQ+LQE G E  P  +A +M MPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED 
Sbjct: 472  SRQMLQEMGREATPEELAERMGMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDS 531

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
             +  P D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRER
Sbjct: 532  TLELPLDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 591

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLE 1428
            IRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 592  IRQIEAKALRKLRHPSRSETLRSFLD 617



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 293/613 (47%), Positives = 412/613 (67%), Gaps = 37/613 (6%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V +   D +
Sbjct: 4   NPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDTDQIEDIIQMINDMGIQVLDSAPDAD 63

Query: 98  TLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
            LML+ NI  +D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKR
Sbjct: 64  DLMLNENIADEDAVEEATQV-LSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+ ++  A++  P  +  ++   +++    +++ +I+ G +D N  +    +   ++
Sbjct: 123 IEDGINEVQSAVAEYPEALAYLIEQYEQVEDGSVRLADIITGFVDPNAIAEEEHLSELED 182

Query: 217 NNEEKILIESSS------------------------ADLSTEQLEKLKYESLIKFSNISF 252
              E+  +++ +                         +++ E+   LK +     + I+ 
Sbjct: 183 ELSEEAEVDTDALDDEDDEESDDSDSSSDDGDNSIDPEVAREKFTALKEQCEKTLATIAK 242

Query: 253 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
           H         + G  S+  I+A ++I  +    R   +  + L  ++R+ + +V   E+Q
Sbjct: 243 HG--------RTGKKSKEQIQALSDIFTQF---RLVPRQFDTLVLSMRSIMKRVRTEERQ 291

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
           I  + V+   MP+ +F+K F   E +  W+D     +  +   L +  P I+    +L  
Sbjct: 292 IQRLAVDYAKMPKEYFLKAFIGKENSEAWLDKLLDGKKPFVEKLQQRAPDIRISIGRLQQ 351

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
           ++ D  L +  +RDI  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 352 IEQDTNLTVQQIRDIGERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 411

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 412 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 471

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SRQ+LQE G E  P  +A +M MPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED 
Sbjct: 472 SRQMLQEMGREATPEELAERMGMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDS 531

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
            +  P D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRER
Sbjct: 532 TLELPLDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 591

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 592 IRQIEAKALRKLR 604


>gi|350530164|ref|ZP_08909105.1| RNA polymerase sigma factor RpoD [Vibrio rotiferianus DAT722]
          Length = 620

 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/617 (50%), Positives = 413/617 (66%), Gaps = 15/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDNNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123  KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTTAPTATH 182

Query: 1005 KNN--NEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAF 1051
              +   E ++  E        E  +    +           +L KF+ +   +  ++ A 
Sbjct: 183  IGSELTESQLEDEDDEDVDEDEDGDDSDDDAEEDVGIDPELALEKFNQLRSTYQNLQLAI 242

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++  V   
Sbjct: 243  NEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYG 302

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  FI +F  NE    W+D        Y   + RN   I+    KL  ++ +  L +
Sbjct: 303  KMPKKSFIALFTGNESTDAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTV 362

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
             +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363  QNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483  REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPVDSA 542

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543  TMTSLKGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 603  RKLRHPSRSETLRSFLD 619



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 404/604 (66%), Gaps = 15/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDNNITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123 KRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTTAPTATH 182

Query: 215 KNN--NEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAF 261
             +   E ++  E        E  +    +           +L KF+ +   +  ++ A 
Sbjct: 183 IGSELTESQLEDEDDEDVDEDEDGDDSDDDAEEDVGIDPELALEKFNQLRSTYQNLQLAI 242

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++  V   
Sbjct: 243 NEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTSMDRVRTQERLIMKSTVEYG 302

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  FI +F  NE    W+D        Y   + RN   I+    KL  ++ +  L +
Sbjct: 303 KMPKKSFIALFTGNESTDAWLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIENETSLTV 362

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363 QNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483 REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPVDSA 542

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543 TMTSLKGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 622 RKLR 625
           RKLR
Sbjct: 603 RKLR 606


>gi|212555455|gb|ACJ27909.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
          Length = 612

 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 305/601 (50%), Positives = 405/601 (67%), Gaps = 4/601 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 1007
              +  +++  P  I  IL   D+    E+++ +I+ G ID N      +   V     + 
Sbjct: 131  NTVQASVAEYPQAIAMILEQFDRFEAEEVRLSDIISGFIDPNAEDVAPTATHVGSELSDE 190

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
              +    +    D           E+  KF+ +    ++  +    +G        A   
Sbjct: 191  ELDDEDDDEDDEDEEEGPKGPDPEEAKEKFTTLRVAHERALEIISIKGRGHPESTVALFE 250

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            I       R   K  ++L  ++R  +++V   E+ I+++ V +  MP+ +F+KV+  NE 
Sbjct: 251  IGEIFKEFRLMPKQFDRLVKSMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNES 310

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            ++ W + E      Y   L      ++  + KL  ++T+  L +  ++DINR+M  GE K
Sbjct: 311  SIEWFNEELASGKPYAEGLKMVDYDVQRCRAKLDAIETETGLAIGAIKDINRRMSIGEAK 370

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 371  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE
Sbjct: 431  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPE 490

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   ++L  L
Sbjct: 491  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGL 550

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK FL
Sbjct: 551  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFL 610

Query: 1428 E 1428
            +
Sbjct: 611  D 611



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 297/588 (50%), Positives = 396/588 (67%), Gaps = 4/588 (0%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 217
             +  +++  P  I  IL   D+    E+++ +I+ G ID N      +   V     + 
Sbjct: 131 NTVQASVAEYPQAIAMILEQFDRFEAEEVRLSDIISGFIDPNAEDVAPTATHVGSELSDE 190

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
             +    +    D           E+  KF+ +    ++  +    +G        A   
Sbjct: 191 ELDDEDDDEDDEDEEEGPKGPDPEEAKEKFTTLRVAHERALEIISIKGRGHPESTVALFE 250

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           I       R   K  ++L  ++R  +++V   E+ I+++ V +  MP+ +F+KV+  NE 
Sbjct: 251 IGEIFKEFRLMPKQFDRLVKSMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNES 310

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           ++ W + E      Y   L      ++  + KL  ++T+  L +  ++DINR+M  GE K
Sbjct: 311 SIEWFNEELASGKPYAEGLKMVDYDVQRCRAKLDAIETETGLAIGAIKDINRRMSIGEAK 370

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 371 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE
Sbjct: 431 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPE 490

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   ++L  L
Sbjct: 491 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAGL 550

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|419256662|ref|ZP_13799167.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10A]
 gi|378098551|gb|EHW60287.1| sigma70 factor RNA polymerase, sigma 70 (sigma D) factor [Escherichia
            coli DEC10A]
          Length = 613

 Score =  572 bits (1473), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 299/610 (49%), Positives = 411/610 (67%), Gaps = 8/610 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63   DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123  IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
            +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183  SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
             +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243  AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303  ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363  RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483  LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               D+L  LT RE+KVLRMRFGI+M++ HTLEEVGKQFDVTRERIRQIEAKALRKL HPS
Sbjct: 543  ATHDVLAGLTAREAKVLRMRFGIDMNTYHTLEEVGKQFDVTRERIRQIEAKALRKLCHPS 602

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 603  RSEVLRSFLD 612



 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 292/596 (48%), Positives = 402/596 (67%), Gaps = 8/596 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           + LML+  T+D+D  EA    LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKR
Sbjct: 63  DDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKR 122

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE+G+  +  +++  P  I  +L   D++   E ++ +++ G +D N   +      +  
Sbjct: 123 IEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVG 182

Query: 217 NNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHFDKMRKAFEKEGYNS 268
           +   +  ++    +   +  +    +        +  KF+ +   +   R   + +G + 
Sbjct: 183 SELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSH 242

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
            +  +    +S      R   K  + L +++R  +++V   E+ I+++ V +C MP+ +F
Sbjct: 243 AAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF 302

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I +F  NE +  W +    +   ++  L      +    QKL  ++ +  L +  ++DIN
Sbjct: 303 ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDIN 362

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 422

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  
Sbjct: 423 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
              D+L  LT RE+KVLRMRFGI+M++ HTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTYHTLEEVGKQFDVTRERIRQIEAKALRKL 598


>gi|399911985|ref|ZP_10780299.1| RNA polymerase sigma factor RpoD [Halomonas sp. KM-1]
          Length = 622

 Score =  571 bits (1472), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 312/619 (50%), Positives = 409/619 (66%), Gaps = 29/619 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 10   RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVVEEAPDEDTLMM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70   SDHSADESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            ++++ A++  P  +  IL A D     E   ++ ++  G ID +       I G      
Sbjct: 130  REVMSALAWLPGAVDSILEAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEAEV 184

Query: 1010 EKILIE--------------------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
             + L++                    +S A+ ST   +    E+  +F  I    + +R+
Sbjct: 185  PEELVDDGAADDADDADADDDEDDADTSEAEESTGGPDP--EEARARFEQIREQNELVRE 242

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
            A  K G  SE      + ++     I+   K  E+L   +R  + Q+   EK ++++ V 
Sbjct: 243  ALAKHGRGSEQARVEMDRLAELFSPIKLVPKHFERLVGQVRISVEQIRTQEKAVMQLFVK 302

Query: 1110 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 1169
               +PR  FIK FP NE    W+D        +   L      I+  Q+++   +  + L
Sbjct: 303  LAKVPRKSFIKAFPGNESRQEWLDEFIAENAKFAERLEPLRADIQRAQRRIAFEEEMVQL 362

Query: 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 1229
            P+ +L++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 363  PVPELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 422

Query: 1230 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 1289
            KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE
Sbjct: 423  KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQE 482

Query: 1290 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349
             G EP P  +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  M  P D
Sbjct: 483  MGREPTPEELGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTMQLPVD 542

Query: 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409
             A    +    +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 543  LATGEGLIEATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 602

Query: 1410 ALRKLRHPSRYYKLKIFLE 1428
            ALRKLRHPSR   L+ FL+
Sbjct: 603  ALRKLRHPSRSEPLRSFLD 621



 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 305/606 (50%), Positives = 400/606 (66%), Gaps = 29/606 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LPEDI D + +E II     M ISV E   D +TLM+
Sbjct: 10  RLKELIARGKEQGYLTYAEVNDHLPEDIADPDQVEDIIGMINDMGISVVEEAPDEDTLMM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S+ ++D+   E   AAL+ V+SD GRT DP++MYMREMG+VELLTR+GEIEIAKRIEEG 
Sbjct: 70  SDHSADESAAEEAVAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEEGT 129

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEI--KIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           ++++ A++  P  +  IL A D     E   ++ ++  G ID +       I G      
Sbjct: 130 REVMSALAWLPGAVDSILEAYDATQDEEAPGRLSDLFSGFIDPDEG-----IPGVAEAEV 184

Query: 220 EKILIE--------------------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
            + L++                    +S A+ ST   +    E+  +F  I    + +R+
Sbjct: 185 PEELVDDGAADDADDADADDDEDDADTSEAEESTGGPDP--EEARARFEQIREQNELVRE 242

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
           A  K G  SE      + ++     I+   K  E+L   +R  + Q+   EK ++++ V 
Sbjct: 243 ALAKHGRGSEQARVEMDRLAELFSPIKLVPKHFERLVGQVRISVEQIRTQEKAVMQLFVK 302

Query: 320 KCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVL 379
              +PR  FIK FP NE    W+D        +   L      I+  Q+++   +  + L
Sbjct: 303 LAKVPRKSFIKAFPGNESRQEWLDEFIAENAKFAERLEPLRADIQRAQRRIAFEEEMVQL 362

Query: 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439
           P+ +L++INR++  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLM
Sbjct: 363 PVPELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 422

Query: 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQE 499
           KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE
Sbjct: 423 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQE 482

Query: 500 TGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559
            G EP P  +  ++EMPE+K+RK++KIAKEP+SME+P+GDD+DSHLGDFIED  M  P D
Sbjct: 483 MGREPTPEELGERLEMPEDKVRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTMQLPVD 542

Query: 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619
            A    +    +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAK
Sbjct: 543 LATGEGLIEATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 602

Query: 620 ALRKLR 625
           ALRKLR
Sbjct: 603 ALRKLR 608


>gi|163802687|ref|ZP_02196578.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
 gi|159173575|gb|EDP58395.1| RNA polymerase sigma factor RpoD [Vibrio sp. AND4]
          Length = 620

 Score =  571 bits (1472), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 310/618 (50%), Positives = 414/618 (66%), Gaps = 17/618 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTAT 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-------------SLIKFSNISFHFDKMRKA 1050
            +  +   +  ++   ++   +  E                  +L KFS +   +  ++ A
Sbjct: 182  HIGSELTETQLKEEDSEDVDDDEESDDDSDDSEEDAGIDPELALEKFSQLRNTYQNLQLA 241

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 1110
              + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++  V  
Sbjct: 242  INEHGYESPKATLANELMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSTVEY 301

Query: 1111 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
              MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L 
Sbjct: 302  GKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRSEEDIRRSITKLKMIEEETSLN 361

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362  VQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 422  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 481

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+
Sbjct: 482  GREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 541

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542  ATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FL+
Sbjct: 602  LRKLRHPSRSETLRSFLD 619



 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/605 (50%), Positives = 405/605 (66%), Gaps = 17/605 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D +          
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPDADDTAAPTAT 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-------------SLIKFSNISFHFDKMRKA 260
           +  +   +  ++   ++   +  E                  +L KFS +   +  ++ A
Sbjct: 182 HIGSELTETQLKEEDSEDVDDDEESDDDSDDSEEDAGIDPELALEKFSQLRNTYQNLQLA 241

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNK 320
             + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++  V  
Sbjct: 242 INEHGYESPKATLANELMLDVFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSTVEY 301

Query: 321 CGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
             MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L 
Sbjct: 302 GKMPKKSFIALFTGNESSEAWLDEILASDKPYAEKIKRSEEDIRRSITKLKMIEEETSLN 361

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 362 VQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 421

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE 
Sbjct: 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM 481

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+
Sbjct: 482 GREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 541

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 542 ATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 601

Query: 621 LRKLR 625
           LRKLR
Sbjct: 602 LRKLR 606


>gi|240948851|ref|ZP_04753207.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
 gi|240296666|gb|EER47277.1| RNA polymerase sigma factor RpoD [Actinobacillus minor NM305]
          Length = 621

 Score =  571 bits (1472), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 406/610 (66%), Gaps = 12/610 (1%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12   QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72   MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 1008
            EG+ ++  A++  P  ++ +L    ++   E+++ +++   +D N      + +    ++
Sbjct: 131  EGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLITAFVDPNAQEEAPIDEDAHLDD 190

Query: 1009 EEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNS 1058
            EE  ++     +   E  +     +            KF+ +    +K   A +K G   
Sbjct: 191  EESDIVADVDDESEDEDGDSSSDNADDSSIDPELAREKFAALKAQHEKALLAIQKHGRTH 250

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
                +  N +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F
Sbjct: 251  AKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADF 310

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +K F  NE    W++     +      L   +  I+     L NL+    L +  +R+I 
Sbjct: 311  LKAFQNNETTEAWIEKAINAKKGGVPKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIG 370

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371  GRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 431  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 490

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 491  LAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 550

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 551  ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 611  RSETLRSFLD 620



 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/597 (49%), Positives = 397/597 (66%), Gaps = 12/597 (2%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12  QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72  MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
           EG+ ++  A++  P  ++ +L    ++   E+++ +++   +D N      + +    ++
Sbjct: 131 EGINEVQCAVAEYPEALVGVLECYAQVEAGEMRLVDLITAFVDPNAQEEAPIDEDAHLDD 190

Query: 219 EEKILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNS 268
           EE  ++     +   E  +     +            KF+ +    +K   A +K G   
Sbjct: 191 EESDIVADVDDESEDEDGDSSSDNADDSSIDPELAREKFAALKAQHEKALLAIQKHGRTH 250

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
               +  N +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F
Sbjct: 251 AKAREQINALSDIFREFRLVPKQFDLLVGSMQKLMKQVRAEERQIQRYAVEYAGMKKADF 310

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           +K F  NE    W++     +      L   +  I+     L NL+    L +  +R+I 
Sbjct: 311 LKAFQNNETTEAWIEKAINAKKGGVPKLANYVEKIRINIVNLQNLEQQSGLTIAQIREIG 370

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
            ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371 GRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 431 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 490

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 491 LAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 550

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 607


>gi|400406351|ref|YP_006589099.1| RNA polymerase sigma factor, sigma-70 family [secondary endosymbiont
            of Heteropsylla cubana]
 gi|400364604|gb|AFP85671.1| RNA polymerase sigma factor, sigma-70 family [secondary endosymbiont
            of Heteropsylla cubana]
          Length = 615

 Score =  571 bits (1472), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 309/612 (50%), Positives = 418/612 (68%), Gaps = 10/612 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTFSE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L+L+  TSD D + A  A   LS+V+++ GRT DPI+MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLLLAETTSDADEDAAEAAAQVLSSVEAELGRTTDPIRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKG 1003
            KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G +D N   +   ++  
Sbjct: 123  KRIEDGINQVQCSVAEYPEAITYLLDQYDRVESGDARLSDLIIGFVDPNAKEDIPSIVDQ 182

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
              N      L   S  D    + E    ++ I        F  +RK +E   +  ++  +
Sbjct: 183  IANELSPDSLSNHSEEDEEDNEDENTDDDNSIDPILAQKKFVALRKQYEITCHVIKTRGR 242

Query: 1064 AHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +H   ++E+L +       R   K  E L + +R+ +++V   E+ I++  V    MP+ 
Sbjct: 243  SHPKSASEILNLSEVFKEFRLVPKQFEHLVNKMRSMMDRVRIQERLIMKSCVEISKMPKK 302

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +FI +F  +E + +W  +   +   ++  L      + +  +KL  ++ +  L +  ++D
Sbjct: 303  NFIMLFSGHETSTSWFQSALMMNKPWSKNLHEVDADVLKRMKKLRQIEEETGLSIGQVKD 362

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P
Sbjct: 423  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATP 482

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++  P D+A + S+
Sbjct: 483  EELAERMLMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSLELPLDSATSDSL 542

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 543  RSATHDVLAGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 603  PSRSEVLRSFLD 614



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 409/599 (68%), Gaps = 10/599 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTFSE+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVTRGKEQGYLTFSEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEA--ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L+L+  TSD D + A  A   LS+V+++ GRT DPI+MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLLLAETTSDADEDAAEAAAQVLSSVEAELGRTTDPIRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKG 213
           KRIE+G+  +  +++  P  I  +L   D++   + ++ +++ G +D N   +   ++  
Sbjct: 123 KRIEDGINQVQCSVAEYPEAITYLLDQYDRVESGDARLSDLIIGFVDPNAKEDIPSIVDQ 182

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
             N      L   S  D    + E    ++ I        F  +RK +E   +  ++  +
Sbjct: 183 IANELSPDSLSNHSEEDEEDNEDENTDDDNSIDPILAQKKFVALRKQYEITCHVIKTRGR 242

Query: 274 AHNNISNEMLGI-------RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +H   ++E+L +       R   K  E L + +R+ +++V   E+ I++  V    MP+ 
Sbjct: 243 SHPKSASEILNLSEVFKEFRLVPKQFEHLVNKMRSMMDRVRIQERLIMKSCVEISKMPKK 302

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +FI +F  +E + +W  +   +   ++  L      + +  +KL  ++ +  L +  ++D
Sbjct: 303 NFIMLFSGHETSTSWFQSALMMNKPWSKNLHEVDADVLKRMKKLRQIEEETGLSIGQVKD 362

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 363 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 422

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P
Sbjct: 423 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATP 482

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED ++  P D+A + S+
Sbjct: 483 EELAERMLMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTSLELPLDSATSDSL 542

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RS   D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 RSATHDVLAGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|251793982|ref|YP_003008714.1| RNA polymerase sigma factor RpoD [Aggregatibacter aphrophilus NJ8700]
 gi|247535381|gb|ACS98627.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
            aphrophilus NJ8700]
          Length = 623

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/625 (48%), Positives = 410/625 (65%), Gaps = 30/625 (4%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4    NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
             LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64   DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 1005
            EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124  EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 1043
            +++EE      +  D+    L+    +                         KF+ +   
Sbjct: 184  DSDEE------NEEDVGDNGLDDESEDEEDGEENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
              K   + EK G  S+        +S+     R   K  + L  ++R+ + +V   E+ I
Sbjct: 238  HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDMMKRVRAQERFI 297

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
              IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298  QRIVVDNAKMPKSGFQKSFIGHETTDTWLIKALGADKAWSEKLVQYENDLRQAIANLVQI 357

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358  EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478  RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538  LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 598  RQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 293/612 (47%), Positives = 401/612 (65%), Gaps = 30/612 (4%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4   NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
            LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64  DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 215
           EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124 EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 253
           +++EE      +  D+    L+    +                         KF+ +   
Sbjct: 184 DSDEE------NEEDVGDNGLDDESEDEEDGEENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
             K   + EK G  S+        +S+     R   K  + L  ++R+ + +V   E+ I
Sbjct: 238 HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDMMKRVRAQERFI 297

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
             IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298 QRIVVDNAKMPKSGFQKSFIGHETTDTWLIKALGADKAWSEKLVQYENDLRQAIANLVQI 357

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358 EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478 RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538 LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 598 RQIEAKALRKLR 609


>gi|336316628|ref|ZP_08571519.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
            sigma factor, sigma-70 family [Rheinheimera sp. A13L]
 gi|335879055|gb|EGM76963.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
            sigma factor, sigma-70 family [Rheinheimera sp. A13L]
          Length = 616

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/612 (50%), Positives = 406/612 (66%), Gaps = 11/612 (1%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D +
Sbjct: 4    NPQSQLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFETAPDAD 63

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
             L++S+   D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRI
Sbjct: 64   DLIMSDAAPDEDAAEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            E+G+  +  +++  P  I  +L   DK    EI++ +IV   ID N   +      +  +
Sbjct: 124  EDGINQVQTSVAEYPEAITYLLEQWDKFEAEEIRLSDIVTAFIDPNEVDDMAPTATHIGS 183

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGY 1056
            +  +  +    AD+S +  E    +              KF  +   ++  R +  K G 
Sbjct: 184  DVPEEELADEDADISGDDEESEDSDEEADTGPDPEMAREKFGELRTQYEVTRNSIVKNGR 243

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
               +  +    +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ 
Sbjct: 244  EHPTTKEEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERIVMKNCVEYAKMPKK 303

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            +F+K F  NE +  W+D E      Y+  L      +    +KL  ++ +  L +  ++D
Sbjct: 304  NFMKSFSGNENSTAWIDAEIAAGKPYSAKLGEMRDDLFRSVEKLKKIEEETGLSIFKIKD 363

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 424  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 483

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED    +P D+A   S+
Sbjct: 484  EELSERMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTSESPLDSATMESL 543

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 544  KAATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 603

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 604  PSRSEVLKSFLD 615



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 299/599 (49%), Positives = 397/599 (66%), Gaps = 11/599 (1%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLTF+E+ND LP+DIID + IE II+    M I V E   D +
Sbjct: 4   NPQSQLKLLILKGKEQGYLTFAEVNDHLPQDIIDSDQIEDIIRMINDMGIQVFETAPDAD 63

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
            L++S+   D+D  E    AL +VD + GRT DP++MYMREMG+VELLTR+GEI+IAKRI
Sbjct: 64  DLIMSDAAPDEDAAEEAAQALVSVDKELGRTTDPVRMYMREMGTVELLTREGEIDIAKRI 123

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           E+G+  +  +++  P  I  +L   DK    EI++ +IV   ID N   +      +  +
Sbjct: 124 EDGINQVQTSVAEYPEAITYLLEQWDKFEAEEIRLSDIVTAFIDPNEVDDMAPTATHIGS 183

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLI-----------KFSNISFHFDKMRKAFEKEGY 266
           +  +  +    AD+S +  E    +              KF  +   ++  R +  K G 
Sbjct: 184 DVPEEELADEDADISGDDEESEDSDEEADTGPDPEMAREKFGELRTQYEVTRNSIVKNGR 243

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
              +  +    +S      R   K  ++L   +R  +++V   E+ +++  V    MP+ 
Sbjct: 244 EHPTTKEEIEKLSEVFRCFRLVPKQFDRLVKNMREMMDRVRVQERIVMKNCVEYAKMPKK 303

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           +F+K F  NE +  W+D E      Y+  L      +    +KL  ++ +  L +  ++D
Sbjct: 304 NFMKSFSGNENSTAWIDAEIAAGKPYSAKLGEMRDDLFRSVEKLKKIEEETGLSIFKIKD 363

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 424 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSP 483

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED    +P D+A   S+
Sbjct: 484 EELSERMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTSESPLDSATMESL 543

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 KAATNEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|24372864|ref|NP_716906.1| RNA polymerase sigma-70 factor RpoD [Shewanella oneidensis MR-1]
 gi|24346976|gb|AAN54351.1| RNA polymerase sigma-70 factor RpoD [Shewanella oneidensis MR-1]
          Length = 616

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/608 (49%), Positives = 411/608 (67%), Gaps = 11/608 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 1008
              +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 128  NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 187

Query: 1009 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            + +   +    +      +            E+  +FS +   ++   K  + +G     
Sbjct: 188  DLEDEDDEEDDEDEDGDGDGDDDGNKGPDPEEARERFSQLRTAYESALKIIDAKGREHPE 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
             I+A   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 248  SIQALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             F  NE NL+W + E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 308  FFTGNETNLDWFEAEKTSNKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 488  ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
             ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
              LK FL+
Sbjct: 608  EILKSFLD 615



 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/595 (49%), Positives = 402/595 (67%), Gaps = 11/595 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVFEEAPDADDMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNN 218
             +  +++  P  I  IL   D+   +E+++ +I+ G +   +++       I    +  
Sbjct: 128 NTVQSSVAEYPQAIAMILEQYDQYEADELRLSDIISGFVNPDEEDLGPTATHIGSELSEE 187

Query: 219 EEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           + +   +    +      +            E+  +FS +   ++   K  + +G     
Sbjct: 188 DLEDEDDEEDDEDEDGDGDGDDDGNKGPDPEEARERFSQLRTAYESALKIIDAKGREHPE 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
            I+A   I       R   K  ++L  ++R+ +++V   E+ ++++ V +  MP+ +F+K
Sbjct: 248 SIQALFEIGEIFKEFRLVPKQFDRLVKSMRSMMDRVRVQERLLMKLCVEQAKMPKKNFVK 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            F  NE NL+W + E      Y   L      ++  + KL  ++ +  L +  ++DINR+
Sbjct: 308 FFTGNETNLDWFEAEKTSNKPYAEGLRMVEEDVQRCRSKLAAIEEETGLVIAAIKDINRR 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + S++S  
Sbjct: 488 ERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATSESLKSAT 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 HEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|422337067|ref|ZP_16418039.1| RNA polymerase sigma factor rpoD [Aggregatibacter aphrophilus F0387]
 gi|353345619|gb|EHB89910.1| RNA polymerase sigma factor rpoD [Aggregatibacter aphrophilus F0387]
          Length = 623

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 300/625 (48%), Positives = 410/625 (65%), Gaps = 30/625 (4%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4    NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
             LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64   DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 1005
            EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124  EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 1043
            +++EE      +  D+    L+    +                         KF+ +   
Sbjct: 184  DSDEE------NEEDVGDNGLDDESEDEEDGEENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
              K   + EK G  S+        +S+     R   K  + L  ++R+ + +V   E+ I
Sbjct: 238  HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDMMKRVRAQERFI 297

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
              IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298  QRIVVDNAKMPKSGFQKSFIGHETTDTWLIKALGAGKAWSEKLVQYENDLRQAIANLVQI 357

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358  EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478  RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538  LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 598  RQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 293/612 (47%), Positives = 401/612 (65%), Gaps = 30/612 (4%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4   NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
            LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64  DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 215
           EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124 EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 253
           +++EE      +  D+    L+    +                         KF+ +   
Sbjct: 184 DSDEE------NEEDVGDNGLDDESEDEEDGEENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
             K   + EK G  S+        +S+     R   K  + L  ++R+ + +V   E+ I
Sbjct: 238 HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDMMKRVRAQERFI 297

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
             IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298 QRIVVDNAKMPKSGFQKSFIGHETTDTWLIKALGAGKAWSEKLVQYENDLRQAIANLVQI 357

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358 EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478 RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538 LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 598 RQIEAKALRKLR 609


>gi|160872802|ref|ZP_02062934.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
 gi|159121601|gb|EDP46939.1| RNA polymerase sigma factor RpoD (Sigma-70) [Rickettsiella grylli]
          Length = 642

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 311/639 (48%), Positives = 427/639 (66%), Gaps = 35/639 (5%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDII-----DHEIIESIIKTFRYMDISV 879
            + E  + + + LI  GK++G++T++EIND L EDII     +   ++ II     + I V
Sbjct: 2    DFEQQQSRLRELITHGKKQGFVTYAEINDHLLEDIISEAEQEQLQLDEIILMLNDIGIPV 61

Query: 880  SEHVLDTETLMLSNITSDDDVEEATE--AALSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
             E   D ETL+ S+I ++ + E ++E    L  + ++ GRT DP++MYMREMG+VELLTR
Sbjct: 62   YEVPPDMETLLSSSIVNNAEEENSSENVTILGNITTELGRTTDPVRMYMREMGTVELLTR 121

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------ 991
            +GEI++AKRIE+GL+ ++ A++  P  I  IL    +  + EI++++I+ G +D      
Sbjct: 122  EGEIKLAKRIEDGLQAILAALAQYPVNISHILNEYTRYEQQEIRLNDIISGFLDLEELSI 181

Query: 992  -------KNFSS----NNRVIKGNKNNNEE--------KILIESSSADLSTEQLEKLKYE 1032
                   KN +S    + R  + +K  +++        K  I ++  D    +L+     
Sbjct: 182  PLELPSGKNITSTETPDERFNRSDKRTDDKDNDEGDDAKSKISATDDDEGFGELDGGPDP 241

Query: 1033 SL--IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 1090
             L   +F+ +  H++    A +K G + +  IK    +++     +   + ++KL   +R
Sbjct: 242  ELAHTRFAELKAHYEAYIAAQKKWGRHDKKTIKQAVLLADAFTKFKLIPRQLDKLTRNMR 301

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 1150
              + ++   E+ I+ + VN+  MPRL FI  FP+NE N N++      +  Y+  L   +
Sbjct: 302  GLLEKIRLQERIIMRLCVNEAKMPRLLFINTFPKNETNENFLKKHIHAKKSYSSRLKELL 361

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
              I   Q KL  L+  I + + ++++INR+M AGE KAR+AK+EM EANLRLVISIAKKY
Sbjct: 362  APITAAQNKLHELEKTIGMTITEIKEINRQMSAGETKARRAKKEMVEANLRLVISIAKKY 421

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 422  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 481

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD- 1329
            HMIETINK++RISRQILQ TG EP P  ++ KM +PE+KIRKI+KIAKEP+SME+P+GD 
Sbjct: 482  HMIETINKLNRISRQILQATGKEPSPEDLSKKMGLPEDKIRKILKIAKEPISMETPIGDE 541

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D DSHLGDFIED   L+P DAA    +R   + +L SLTPRE+KVLRMRFGI+M++DHTL
Sbjct: 542  DGDSHLGDFIEDAAALSPIDAATIEGLRETAQRVLASLTPREAKVLRMRFGIDMNTDHTL 601

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL+
Sbjct: 602  EEVGKQFDVTRERIRQIEAKALRKLRHPTRSEPLRSFLD 640



 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 305/626 (48%), Positives = 418/626 (66%), Gaps = 35/626 (5%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDII-----DHEIIESIIKTFRYMDISV 89
           + E  + + + LI  GK++G++T++EIND L EDII     +   ++ II     + I V
Sbjct: 2   DFEQQQSRLRELITHGKKQGFVTYAEINDHLLEDIISEAEQEQLQLDEIILMLNDIGIPV 61

Query: 90  SEHVLDTETLMLSNITSDDDVEEATE--AALSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
            E   D ETL+ S+I ++ + E ++E    L  + ++ GRT DP++MYMREMG+VELLTR
Sbjct: 62  YEVPPDMETLLSSSIVNNAEEENSSENVTILGNITTELGRTTDPVRMYMREMGTVELLTR 121

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID------ 201
           +GEI++AKRIE+GL+ ++ A++  P  I  IL    +  + EI++++I+ G +D      
Sbjct: 122 EGEIKLAKRIEDGLQAILAALAQYPVNISHILNEYTRYEQQEIRLNDIISGFLDLEELSI 181

Query: 202 -------KNFSS----NNRVIKGNKNNNEE--------KILIESSSADLSTEQLEKLKYE 242
                  KN +S    + R  + +K  +++        K  I ++  D    +L+     
Sbjct: 182 PLELPSGKNITSTETPDERFNRSDKRTDDKDNDEGDDAKSKISATDDDEGFGELDGGPDP 241

Query: 243 SL--IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLR 300
            L   +F+ +  H++    A +K G + +  IK    +++     +   + ++KL   +R
Sbjct: 242 ELAHTRFAELKAHYEAYIAAQKKWGRHDKKTIKQAVLLADAFTKFKLIPRQLDKLTRNMR 301

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNI 360
             + ++   E+ I+ + VN+  MPRL FI  FP+NE N N++      +  Y+  L   +
Sbjct: 302 GLLEKIRLQERIIMRLCVNEAKMPRLLFINTFPKNETNENFLKKHIHAKKSYSSRLKELL 361

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
             I   Q KL  L+  I + + ++++INR+M AGE KAR+AK+EM EANLRLVISIAKKY
Sbjct: 362 APITAAQNKLHELEKTIGMTITEIKEINRQMSAGETKARRAKKEMVEANLRLVISIAKKY 421

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 422 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 481

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD- 539
           HMIETINK++RISRQILQ TG EP P  ++ KM +PE+KIRKI+KIAKEP+SME+P+GD 
Sbjct: 482 HMIETINKLNRISRQILQATGKEPSPEDLSKKMGLPEDKIRKILKIAKEPISMETPIGDE 541

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D DSHLGDFIED   L+P DAA    +R   + +L SLTPRE+KVLRMRFGI+M++DHTL
Sbjct: 542 DGDSHLGDFIEDAAALSPIDAATIEGLRETAQRVLASLTPREAKVLRMRFGIDMNTDHTL 601

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 602 EEVGKQFDVTRERIRQIEAKALRKLR 627


>gi|425063934|ref|ZP_18467059.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            gallicida X73]
 gi|404382488|gb|EJZ78949.1| RNA polymerase sigma factor RpoD [Pasteurella multocida subsp.
            gallicida X73]
          Length = 622

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 309/623 (49%), Positives = 416/623 (66%), Gaps = 25/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 887  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 1003
            RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122  RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 1045
                +E+    +S  A L+ E+ E+ + E                     KF  +     
Sbjct: 182  TFAEDEDS---DSVGATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239  KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
            IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299  IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359  QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479  MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539  LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 599  IEAKALRKLRHPSRSETLRSFLD 621



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 302/610 (49%), Positives = 407/610 (66%), Gaps = 25/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLESAPDA 62

Query: 97  ETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LML+   +D+D VEEAT+  LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLNETIADEDAVEEATQV-LSSVEAEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKG 213
           RIEEG+ ++  AI+  P  I  +L     + +  +++ +++ G +D N  +   V  I+ 
Sbjct: 122 RIEEGINEVQSAIAFYPEAISYLLDQYALVEEGGVRLADLITGFVDPNAMTEGDVAEIED 181

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFD 255
               +E+    +S  A L+ E+ E+ + E                     KF  +     
Sbjct: 182 TFAEDEDS---DSVGATLNEEEEEEEESEEESTTDDSDSDNSIDPEVAREKFLELKTQHA 238

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K     EK G  S+        +++     R   K  + L + + N +  V   E+ I +
Sbjct: 239 KAVAMIEKHGRTSKKSKDQIQALADVFTQFRLVPKQFDTLVNLMSNMMKSVRLQERSIQK 298

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
           IVV+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++ 
Sbjct: 299 IVVDKAKMPKEQFQKVFIGHENKDTWLVKALSSGKTWSEKLAKHEEEIRYYIDNILEIER 358

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L ++ +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 359 QTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 418

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 419 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 478

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  + 
Sbjct: 479 MLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLE 538

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 539 LPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 598

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 599 IEAKALRKLR 608


>gi|378823729|ref|ZP_09846327.1| RNA polymerase sigma factor RpoD, partial [Sutterella parvirubra
           YIT 11816]
 gi|378597450|gb|EHY30740.1| RNA polymerase sigma factor RpoD, partial [Sutterella parvirubra
           YIT 11816]
          Length = 862

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/607 (49%), Positives = 418/607 (68%), Gaps = 26/607 (4%)

Query: 6   KKTKIKNKKTKETLLKNAFS--FDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEIND 63
           K+T+ ++K  +E  L++A +  + ++  S+E   + R K   LI +GKERGY+T+SEIND
Sbjct: 269 KRTR-RSKSAREKALRDAIANGYSVEEESQE---DRRSKLLKLISMGKERGYVTYSEIND 324

Query: 64  FLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALST 120
            +P  +ID + IE+I+     ++I V E   D E L++       S++D E   EAALST
Sbjct: 325 NIPNSLIDDDAIETIVSILSNLNIEVHEVAPDEEQLLMQGSGTPVSEEDAEAEAEAALST 384

Query: 121 VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILI 180
           VDS+FGRT DP+++YMREMGSVELL+R+GEIEI+KRIE+GLK M+ AI+ CP TI E+L 
Sbjct: 385 VDSEFGRTTDPVRIYMREMGSVELLSREGEIEISKRIEDGLKHMVLAIARCPVTIEEVLK 444

Query: 181 AADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLK 240
           +A  I +  + ID++VDG+   +   +  VI+ +   +         ++ ++  QLE+LK
Sbjct: 445 SAAAIREGTMSIDDVVDGITSTDDVGS--VIRADDETD-------MGASAMTVGQLEELK 495

Query: 241 YESLIKFSNISFHFDKMRKAF---EKEGYNSESYIKA-----HNNISNEMLGIRFTAKSI 292
             SL  F  +   F  + + F    ++GY     +KA      + I  +++G+RFTAK+ 
Sbjct: 496 RRSLEVFDRVDAKFKDLCERFREASQQGYAGLDAVKADQEALKDGIQQDLMGLRFTAKTA 555

Query: 293 EKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY 352
           ++LC+TLR  + ++   E+ + + +V   G+ R  F++ F ++  ++ W+D       + 
Sbjct: 556 DRLCETLRVTVGRLRASERIVYDELVRGAGIDRAWFMERFIDHATDVAWLDEVAAAFPEK 615

Query: 353 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 412
              + R    I E Q KL  L+    + +++L D  ++M  GE KAR AKREMTEANLRL
Sbjct: 616 RAQILRRRAPIAEEQHKLAELEQTTFMTVHELLDAYKQMATGEAKARNAKREMTEANLRL 675

Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
           VISIAKKYT+RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 676 VISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 735

Query: 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 532
           ARTIRIPVHMIETIN+++RI+RQ LQETG EPD   +A  M+MPE+KI KIMKIAKEP+S
Sbjct: 736 ARTIRIPVHMIETINRMNRITRQELQETGVEPDSRRLAELMDMPEDKILKIMKIAKEPIS 795

Query: 533 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 592
           ME+P+GDD+DSHLGDF+ED    AP++A  N+S+   VK +L+SL+PRE+KVLRMRFGIE
Sbjct: 796 METPIGDDDDSHLGDFLEDTQTTAPAEAIQNSSLSETVKQVLDSLSPREAKVLRMRFGIE 855

Query: 593 MSSDHTL 599
           M SDHTL
Sbjct: 856 MQSDHTL 862



 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 299/589 (50%), Positives = 405/589 (68%), Gaps = 25/589 (4%)

Query: 812  NAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKT 871
            N +S + +S      E+ R K   LI +GKERGY+T+SEIND +P  +ID + IE+I+  
Sbjct: 288  NGYSVEEESQ-----EDRRSKLLKLISMGKERGYVTYSEINDNIPNSLIDDDAIETIVSI 342

Query: 872  FRYMDISVSEHVLDTETLML---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMRE 928
               ++I V E   D E L++       S++D E   EAALSTVDS+FGRT DP+++YMRE
Sbjct: 343  LSNLNIEVHEVAPDEEQLLMQGSGTPVSEEDAEAEAEAALSTVDSEFGRTTDPVRIYMRE 402

Query: 929  MGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG 988
            MGSVELL+R+GEIEI+KRIE+GLK M+ AI+ CP TI E+L +A  I +  + ID++VDG
Sbjct: 403  MGSVELLSREGEIEISKRIEDGLKHMVLAIARCPVTIEEVLKSAAAIREGTMSIDDVVDG 462

Query: 989  LIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
            +   +   +  VI+ +   +         ++ ++  QLE+LK  SL  F  +   F  + 
Sbjct: 463  ITSTDDVGS--VIRADDETD-------MGASAMTVGQLEELKRRSLEVFDRVDAKFKDLC 513

Query: 1049 KAF---EKEGYNSESYIKA-----HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            + F    ++GY     +KA      + I  +++G+RFTAK+ ++LC+TLR  + ++   E
Sbjct: 514  ERFREASQQGYAGLDAVKADQEALKDGIQQDLMGLRFTAKTADRLCETLRVTVGRLRASE 573

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            + + + +V   G+ R  F++ F ++  ++ W+D       +    + R    I E Q KL
Sbjct: 574  RIVYDELVRGAGIDRAWFMERFIDHATDVAWLDEVAAAFPEKRAQILRRRAPIAEEQHKL 633

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
              L+    + +++L D  ++M  GE KAR AKREMTEANLRLVISIAKKYT+RGLQFLDL
Sbjct: 634  AELEQTTFMTVHELLDAYKQMATGEAKARNAKREMTEANLRLVISIAKKYTNRGLQFLDL 693

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGN+GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN+++
Sbjct: 694  IQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINRMN 753

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RI+RQ LQETG EPD   +A  M+MPE+KI KIMKIAKEP+SME+P+GDD+DSHLGDF+E
Sbjct: 754  RITRQELQETGVEPDSRRLAELMDMPEDKILKIMKIAKEPISMETPIGDDDDSHLGDFLE 813

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D    AP++A  N+S+   VK +L+SL+PRE+KVLRMRFGIEM SDHTL
Sbjct: 814  DTQTTAPAEAIQNSSLSETVKQVLDSLSPREAKVLRMRFGIEMQSDHTL 862


>gi|424047983|ref|ZP_17785539.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HENC-03]
 gi|408883293|gb|EKM22080.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HENC-03]
          Length = 620

 Score =  571 bits (1471), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 313/622 (50%), Positives = 418/622 (67%), Gaps = 25/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-AEDTAAPTA 180

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 1046
                +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 181  THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDAEEDVGIDPELALEKFNQLRSTYQN 237

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238  LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKA 297

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +
Sbjct: 298  AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRSEEEIRRSITKLKMIEEE 357

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358  TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538  PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 598  EAKALRKLRHPSRSETLRSFLD 619



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 409/609 (67%), Gaps = 25/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 122 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-AEDTAAPTA 180

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 256
               +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 181 THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDAEEDVGIDPELALEKFNQLRSTYQN 237

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 238 LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKA 297

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +
Sbjct: 298 AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRSEEEIRRSITKLKMIEEE 357

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 358 TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 417

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 418 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 477

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 478 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 537

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 538 PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 597

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 598 EAKALRKLR 606


>gi|117618585|ref|YP_855378.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
            hydrophila ATCC 7966]
 gi|117559992|gb|ABK36940.1| RNA polymerase sigma factor RpoD [Aeromonas hydrophila subsp.
            hydrophila ATCC 7966]
          Length = 618

 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/613 (49%), Positives = 415/613 (67%), Gaps = 19/613 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 995
            +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETDDVAPTATHIGSELS 187

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
              +   +    + +E    + S  D       ++  E   KF ++   ++  R + ++ G
Sbjct: 188  EEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVARE---KFGDLRAQYEVTRLSIQQNG 244

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245  RAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              F+  F  NE    W + + +    ++  L      +     KL  ++ +  L +  ++
Sbjct: 305  KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDVLRAIGKLQQIEEETGLSIAQIK 364

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+
Sbjct: 425  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPN 484

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S
Sbjct: 485  PEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSES 544

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545  LRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 605  HPSRSEVLRSFLD 617



 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/600 (49%), Positives = 406/600 (67%), Gaps = 19/600 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 205
           +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETDDVAPTATHIGSELS 187

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
             +   +    + +E    + S  D       ++  E   KF ++   ++  R + ++ G
Sbjct: 188 EEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVARE---KFGDLRAQYEVTRLSIQQNG 244

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245 RAHEDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             F+  F  NE    W + + +    ++  L      +     KL  ++ +  L +  ++
Sbjct: 305 KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDVLRAIGKLQQIEEETGLSIAQIK 364

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+
Sbjct: 425 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPN 484

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S
Sbjct: 485 PEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSES 544

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 LRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|357416622|ref|YP_004929642.1| RNA polymerase sigma factor RpoD [Pseudoxanthomonas spadix BD-a59]
 gi|355334200|gb|AER55601.1| RNA polymerase sigma factor RpoD [Pseudoxanthomonas spadix BD-a59]
          Length = 621

 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/608 (49%), Positives = 409/608 (67%), Gaps = 12/608 (1%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I+V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIAVHEVAPDAETLLLA 71

Query: 893  NITS-----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
               S     D+   E   AAL+++D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   GEASGNREVDETAAEEAAAALTSLDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            EEGL  +  ++   P+ I  +L   +     + ++ E++ G  D+        +  +  +
Sbjct: 132  EEGLGKVQASLGLLPSIIESVLEDYELHKAGKKRLAEVIVGFNDQVDEPEPPAVVADAVD 191

Query: 1008 NEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
              ++   ES   ++  +  E+          E   +   ++    K +K + K G ++++
Sbjct: 192  ATDEADAESVDEEVDEDAAEEEAGPTGPDPEEVARRMEVLASTLAKFKKGYAKAGADNKA 251

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              K    +++  + ++      + L   +R  + Q+   E+++L +      MPR  FI+
Sbjct: 252  GAKLRAEMADMFVTLKLPLALTDTLVKNVREVLQQIKDQERRVLHLSTVTAKMPRKDFIR 311

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WVD   K +  ++  L      I   Q+  I ++  + + L +L+DI+R+
Sbjct: 312  SWEGNQTNLEWVDEALKRKQKWSSGLREVKDQIIAEQRATIAVEQAMFMSLAELKDISRQ 371

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 372  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 431

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 432  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 491

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 492  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPVENTTNINLMETV 551

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 552  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 611

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 612  ETLRSFLD 619



 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/595 (49%), Positives = 400/595 (67%), Gaps = 12/595 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I+V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIAVHEVAPDAETLLLA 71

Query: 103 NITS-----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
              S     D+   E   AAL+++D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  GEASGNREVDETAAEEAAAALTSLDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           EEGL  +  ++   P+ I  +L   +     + ++ E++ G  D+        +  +  +
Sbjct: 132 EEGLGKVQASLGLLPSIIESVLEDYELHKAGKKRLAEVIVGFNDQVDEPEPPAVVADAVD 191

Query: 218 NEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSES 270
             ++   ES   ++  +  E+          E   +   ++    K +K + K G ++++
Sbjct: 192 ATDEADAESVDEEVDEDAAEEEAGPTGPDPEEVARRMEVLASTLAKFKKGYAKAGADNKA 251

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             K    +++  + ++      + L   +R  + Q+   E+++L +      MPR  FI+
Sbjct: 252 GAKLRAEMADMFVTLKLPLALTDTLVKNVREVLQQIKDQERRVLHLSTVTAKMPRKDFIR 311

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WVD   K +  ++  L      I   Q+  I ++  + + L +L+DI+R+
Sbjct: 312 SWEGNQTNLEWVDEALKRKQKWSSGLREVKDQIIAEQRATIAVEQAMFMSLAELKDISRQ 371

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 372 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 431

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 432 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 491

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 492 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPVENTTNINLMETV 551

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|269960187|ref|ZP_06174562.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
 gi|269834994|gb|EEZ89078.1| RNA polymerase sigma factor [Vibrio harveyi 1DA3]
          Length = 639

 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 313/622 (50%), Positives = 418/622 (67%), Gaps = 25/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 883
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 22   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 81

Query: 884  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 82   DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 140

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 141  AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 199

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 1046
                +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 200  THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 256

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 257  LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKA 316

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +
Sbjct: 317  AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRSEEEIRRSITKLKMIEEE 376

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 377  TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 436

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 437  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 496

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 497  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 556

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 557  PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 616

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 617  EAKALRKLRHPSRSETLRSFLD 638



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 409/609 (67%), Gaps = 25/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--- 93
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 22  QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 81

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D      +NIT +D   EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 82  DDLALNDDTNITDED-AAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 140

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIEEG+  +  +++  P TI  IL   DK+   E+++ +++ G +D + + +      
Sbjct: 141 AKRIEEGINQVQSSVAEYPGTIPYILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTA 199

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----------------SLIKFSNISFHFDK 256
               +E   L ES   +   E +++ +                   +L KF+ +   +  
Sbjct: 200 THIGSE---LTESQLEEEDEEDVDEDEESDDDSDDSEEDVGIDPELALEKFNQLRSTYQN 256

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++ A  + GY S     A+  + +     R T K  + L + LR  +++V   E+ I++ 
Sbjct: 257 LQLAINEHGYESPKATVANELMLDVFKEFRLTPKQFDHLVNELRTAMDRVRTQERLIMKA 316

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +
Sbjct: 317 AVEYGKMPKKSFIALFTGNESSEAWLDEILSSDKPYAEKIKRSEEEIRRSITKLKMIEEE 376

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 377 TSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 436

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 496

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 497 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 556

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 557 PLDSATATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 616

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 617 EAKALRKLR 625


>gi|377812057|ref|YP_005044497.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. YI23]
 gi|357941418|gb|AET94974.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. YI23]
          Length = 648

 Score =  570 bits (1470), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 280/634 (44%), Positives = 422/634 (66%), Gaps = 16/634 (2%)

Query: 800  IRKFGYKIFSKKNAFSFD-IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPED 858
            +++ G+ +   +   S D +KS+ ++  +      + LI++GK++G++T ++IND LP D
Sbjct: 25   LKRAGWPLV--ETPISADPVKSDRQQGTDEHEWAIRALIRIGKDQGFVTHAQINDHLPGD 82

Query: 859  IIDHEIIESIIKTFRYMDISVSEHVLDTETLML----SNITSDDDVEEATEAALSTVDSD 914
            +    ++E I + F  M ++V EH   TETL+L    SN T DD   E  E ALS VDS+
Sbjct: 83   LAQMTMVEDISRAFHEMGLAVYEHAPSTETLLLDDAVSNDTLDDQSGEDDEFALSAVDSE 142

Query: 915  FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADK 974
            FGRT DP++MYMREMG+ +LLTR  E+EIA+RIE+ L +MI AI+SCP TI  IL +A  
Sbjct: 143  FGRTTDPVRMYMREMGAKQLLTRKAEVEIARRIEDSLNEMIQAIASCPPTISMILASAQL 202

Query: 975  ISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESL 1034
            +++ ++ IDE++DG+ D++  +   V +   +N +     E ++  L   +L +L  + L
Sbjct: 203  VAEGKLGIDEMIDGIDDESMPAAAEVDESAPHNCQSDSEAEDNADQL---RLTRLMTDGL 259

Query: 1035 IKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQIN 1094
              F  +    D++R+A E    N      A   I  E+  +RFTA+ + + CD ++ ++ 
Sbjct: 260  ALFGRVRECVDQLREAGETHAPN------ALETIRKELGRVRFTARIVGQACDDMQQRLA 313

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
            +V QIE++I  I +++C MPR  FI +FP +E +L+W         DY   L R++ +++
Sbjct: 314  RVRQIEQRISSIAIDRCSMPREQFIALFPGHETDLDWTTKTAAKSLDYGASLERSVAAVR 373

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
              Q +L++++    +P+  L+  +R ++A E + R+AK EM EANLRLVISIAKKY +RG
Sbjct: 374  AEQYQLMDIERHAAMPIQRLKQTSRHLLAAESRMRRAKDEMIEANLRLVISIAKKYVNRG 433

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            + FLDLIQEGNIGLMKAVDKFEY+RG+KFSTYATWW+RQA+TR++ADQART+RIPVHM+E
Sbjct: 434  VHFLDLIQEGNIGLMKAVDKFEYKRGWKFSTYATWWVRQAVTRAVADQARTVRIPVHMME 493

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
             INK++RIS ++ Q TG    P+ +A +ME+PE +IR I K+A  P+S+++P  DD D+ 
Sbjct: 494  IINKLNRISNELRQHTGKPALPAALAERMELPEAQIRGIQKMAMHPISLQTPANDDADAT 553

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGD IED N+ +P +  +   MR  + D LN+L PRE++VLRMRFGI + ++ TL EV  
Sbjct: 554  LGDLIEDANVKSPLEVVVRTGMRVAIDDALNTLLPREARVLRMRFGINVPTEFTLGEVSS 613

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
               V+RER+RQIE++A+RKL HPSR  KL+ F++
Sbjct: 614  HLGVSRERVRQIESQAIRKLMHPSRADKLRSFID 647



 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 274/617 (44%), Positives = 410/617 (66%), Gaps = 14/617 (2%)

Query: 13  KKTKETLLKNAFSFD-IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIID 71
           K+    L++   S D +KS+ ++  +      + LI++GK++G++T ++IND LP D+  
Sbjct: 26  KRAGWPLVETPISADPVKSDRQQGTDEHEWAIRALIRIGKDQGFVTHAQINDHLPGDLAQ 85

Query: 72  HEIIESIIKTFRYMDISVSEHVLDTETLML----SNITSDDDVEEATEAALSTVDSDFGR 127
             ++E I + F  M ++V EH   TETL+L    SN T DD   E  E ALS VDS+FGR
Sbjct: 86  MTMVEDISRAFHEMGLAVYEHAPSTETLLLDDAVSNDTLDDQSGEDDEFALSAVDSEFGR 145

Query: 128 TKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISK 187
           T DP++MYMREMG+ +LLTR  E+EIA+RIE+ L +MI AI+SCP TI  IL +A  +++
Sbjct: 146 TTDPVRMYMREMGAKQLLTRKAEVEIARRIEDSLNEMIQAIASCPPTISMILASAQLVAE 205

Query: 188 NEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKF 247
            ++ IDE++DG+ D++  +   V +   +N +     E ++  L   +L +L  + L  F
Sbjct: 206 GKLGIDEMIDGIDDESMPAAAEVDESAPHNCQSDSEAEDNADQL---RLTRLMTDGLALF 262

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
             +    D++R+A E    N      A   I  E+  +RFTA+ + + CD ++ ++ +V 
Sbjct: 263 GRVRECVDQLREAGETHAPN------ALETIRKELGRVRFTARIVGQACDDMQQRLARVR 316

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
           QIE++I  I +++C MPR  FI +FP +E +L+W         DY   L R++ +++  Q
Sbjct: 317 QIEQRISSIAIDRCSMPREQFIALFPGHETDLDWTTKTAAKSLDYGASLERSVAAVRAEQ 376

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            +L++++    +P+  L+  +R ++A E + R+AK EM EANLRLVISIAKKY +RG+ F
Sbjct: 377 YQLMDIERHAAMPIQRLKQTSRHLLAAESRMRRAKDEMIEANLRLVISIAKKYVNRGVHF 436

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEY+RG+KFSTYATWW+RQA+TR++ADQART+RIPVHM+E IN
Sbjct: 437 LDLIQEGNIGLMKAVDKFEYKRGWKFSTYATWWVRQAVTRAVADQARTVRIPVHMMEIIN 496

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RIS ++ Q TG    P+ +A +ME+PE +IR I K+A  P+S+++P  DD D+ LGD
Sbjct: 497 KLNRISNELRQHTGKPALPAALAERMELPEAQIRGIQKMAMHPISLQTPANDDADATLGD 556

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
            IED N+ +P +  +   MR  + D LN+L PRE++VLRMRFGI + ++ TL EV     
Sbjct: 557 LIEDANVKSPLEVVVRTGMRVAIDDALNTLLPREARVLRMRFGINVPTEFTLGEVSSHLG 616

Query: 608 VTRERIRQIEAKALRKL 624
           V+RER+RQIE++A+RKL
Sbjct: 617 VSRERVRQIESQAIRKL 633


>gi|384082652|ref|ZP_09993827.1| transcription initiation factor sigma 70 [gamma proteobacterium
            HIMB30]
          Length = 625

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/615 (48%), Positives = 414/615 (67%), Gaps = 13/615 (2%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            + E  + + K LI  GKE+GYLT++E+ND LPE+I D + +E II+    M I+V E   
Sbjct: 12   QTEQRQSRLKELIAKGKEQGYLTYAEVNDHLPEEIADPDQVEDIIRMIGDMGIAVGEEAP 71

Query: 885  DTETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            D + L+L   +  +DD   E   AAL++V++D GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 72   DDDQLLLGENSAATDDSAAEEAAAALASVENDVGRTTDPVRMYMREMGTVELLTREGEIV 131

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEG+++++ A++  P  +  +L   D+I   E ++ +++ G +D + +    V  
Sbjct: 132  IAKRIEEGIREVMQAMAYYPGIVDSVLAIYDRIQSEEGRMSDLLAGFLDPDPADEEPVEA 191

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEK 1053
             +     ++   +S S D   +  +  +          E   +F  +  +  K  K   K
Sbjct: 192  ASTEEVSDQDFDDSDSDDEDDDSDDSDEEEGDTGPDPEEVRARFEALRVNLAKAEKVIAK 251

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
            +G +S+    A N I +    ++ T +  ++LC   R  ++ +   E++IL +   +  +
Sbjct: 252  KGRDSKESKDALNAIGDVFSSLKLTPRLFDELCIEFRTVLDSIRNQEREILRLCTKQGKL 311

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
             R  FIK +  NE N  W+    K +    L     IP ++  Q +L ++   + + + +
Sbjct: 312  DRKVFIKEWHGNETNFEWIPGVAKKKKSEKLEAV--IPDVQRCQARLQSIAEGVGVTIPE 369

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            LR++NR++  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 370  LREVNRRLSMGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 429

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 430  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 489

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A  
Sbjct: 490  PTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSPVDSATV 549

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              +    + +L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 550  EGLTESTRQVLASLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 609

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 610  LRHPSRSDHLRSFLD 624



 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 294/602 (48%), Positives = 405/602 (67%), Gaps = 13/602 (2%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           + E  + + K LI  GKE+GYLT++E+ND LPE+I D + +E II+    M I+V E   
Sbjct: 12  QTEQRQSRLKELIAKGKEQGYLTYAEVNDHLPEEIADPDQVEDIIRMIGDMGIAVGEEAP 71

Query: 95  DTETLMLS--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           D + L+L   +  +DD   E   AAL++V++D GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 72  DDDQLLLGENSAATDDSAAEEAAAALASVENDVGRTTDPVRMYMREMGTVELLTREGEIV 131

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEG+++++ A++  P  +  +L   D+I   E ++ +++ G +D + +    V  
Sbjct: 132 IAKRIEEGIREVMQAMAYYPGIVDSVLAIYDRIQSEEGRMSDLLAGFLDPDPADEEPVEA 191

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKY---------ESLIKFSNISFHFDKMRKAFEK 263
            +     ++   +S S D   +  +  +          E   +F  +  +  K  K   K
Sbjct: 192 ASTEEVSDQDFDDSDSDDEDDDSDDSDEEEGDTGPDPEEVRARFEALRVNLAKAEKVIAK 251

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
           +G +S+    A N I +    ++ T +  ++LC   R  ++ +   E++IL +   +  +
Sbjct: 252 KGRDSKESKDALNAIGDVFSSLKLTPRLFDELCIEFRTVLDSIRNQEREILRLCTKQGKL 311

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
            R  FIK +  NE N  W+    K +    L     IP ++  Q +L ++   + + + +
Sbjct: 312 DRKVFIKEWHGNETNFEWIPGVAKKKKSEKLEAV--IPDVQRCQARLQSIAEGVGVTIPE 369

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           LR++NR++  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 370 LREVNRRLSMGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 429

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 430 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 489

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A  
Sbjct: 490 PTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSPVDSATV 549

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             +    + +L SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 550 EGLTESTRQVLASLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 609

Query: 624 LR 625
           LR
Sbjct: 610 LR 611


>gi|27904560|ref|NP_777686.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
            (Baizongia pistaciae)]
 gi|31340403|sp|Q89B10.1|RPOD_BUCBP RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|27903957|gb|AAO26791.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
            (Baizongia pistaciae)]
          Length = 609

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/617 (49%), Positives = 420/617 (68%), Gaps = 26/617 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT+SEIND L ++II+ + IE II+    M I V E   D+
Sbjct: 3    QNPQSQLKLLVTYGKEQGYLTYSEINDHLSDNIINSDQIEDIIQMINDMGIQVVEKAPDS 62

Query: 887  ETLMLSNIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            + L+L  I     +D+D+ EAT   LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+
Sbjct: 63   DDLILHEIKRNNETDEDIVEATAQVLSTVESELGRTTDPVRMYMREMGTVELLTREGEID 122

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE+G+  +  +++  P  I  +L   +++   E+++ E++ G +D N  + +  I 
Sbjct: 123  IAKRIEDGINQVQCSVAEYPEAITHLLEQYNRVELGELRLSELIHGFVDPNAEAVHTSIT 182

Query: 1003 GNKNNNEEKILIESSSADLSTEQLE-------KLKYESLIKFSNISFHFDKMRKAFEKEG 1055
             + N N E    E    D + E  +       +L  E  I   N  +H      A + + 
Sbjct: 183  NHINTNSE----EHHHNDNTEENNDDDHLVDPELAREKFIALKN-QYHITNY--AIKTKN 235

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             N +  +   NN+S      R   K  + L   +R  + ++   E+ I ++ +    +P+
Sbjct: 236  RNHQDTLIEINNLSEIFKQFRLVPKQFDHLVINMRKMMQKIRIQERNIAKLCIEYGNIPK 295

Query: 1116 LHFIKVFPENEINLNW---VDNETKIQHD-YNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
               +  F   + N  W   V N  K   D +N I     P I+ + +KL  ++ +  L +
Sbjct: 296  KALLNFFSLQKTNQIWSKIVQNIKKPWIDKFNTIK----PDIQMILKKLQKVEEETGLTI 351

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
            + +++IN+++  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 352  HQVKNINKRISLGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 411

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G
Sbjct: 412  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEIG 471

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  ++ +M +PE+KIRK++KIAKEP+SME+P+G+D+DSHLGDF+ED N+  P D+A
Sbjct: 472  REPTPEELSERMLIPEDKIRKVLKIAKEPISMETPIGEDDDSHLGDFLEDTNIELPLDSA 531

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             +AS+RS  K++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 532  TSASLRSATKNVLSGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 591

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 592  RKLRHPSRSEILRSFLD 608



 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 300/604 (49%), Positives = 411/604 (68%), Gaps = 26/604 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT+SEIND L ++II+ + IE II+    M I V E   D+
Sbjct: 3   QNPQSQLKLLVTYGKEQGYLTYSEINDHLSDNIINSDQIEDIIQMINDMGIQVVEKAPDS 62

Query: 97  ETLMLSNIT----SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           + L+L  I     +D+D+ EAT   LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+
Sbjct: 63  DDLILHEIKRNNETDEDIVEATAQVLSTVESELGRTTDPVRMYMREMGTVELLTREGEID 122

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE+G+  +  +++  P  I  +L   +++   E+++ E++ G +D N  + +  I 
Sbjct: 123 IAKRIEDGINQVQCSVAEYPEAITHLLEQYNRVELGELRLSELIHGFVDPNAEAVHTSIT 182

Query: 213 GNKNNNEEKILIESSSADLSTEQLE-------KLKYESLIKFSNISFHFDKMRKAFEKEG 265
            + N N E    E    D + E  +       +L  E  I   N  +H      A + + 
Sbjct: 183 NHINTNSE----EHHHNDNTEENNDDDHLVDPELAREKFIALKN-QYHITNY--AIKTKN 235

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            N +  +   NN+S      R   K  + L   +R  + ++   E+ I ++ +    +P+
Sbjct: 236 RNHQDTLIEINNLSEIFKQFRLVPKQFDHLVINMRKMMQKIRIQERNIAKLCIEYGNIPK 295

Query: 326 LHFIKVFPENEINLNW---VDNETKIQHD-YNLILCRNIPSIKELQQKLINLQTDIVLPL 381
              +  F   + N  W   V N  K   D +N I     P I+ + +KL  ++ +  L +
Sbjct: 296 KALLNFFSLQKTNQIWSKIVQNIKKPWIDKFNTIK----PDIQMILKKLQKVEEETGLTI 351

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
           + +++IN+++  GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 352 HQVKNINKRISLGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 411

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G
Sbjct: 412 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQEIG 471

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  ++ +M +PE+KIRK++KIAKEP+SME+P+G+D+DSHLGDF+ED N+  P D+A
Sbjct: 472 REPTPEELSERMLIPEDKIRKVLKIAKEPISMETPIGEDDDSHLGDFLEDTNIELPLDSA 531

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            +AS+RS  K++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 532 TSASLRSATKNVLSGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 591

Query: 622 RKLR 625
           RKLR
Sbjct: 592 RKLR 595


>gi|410637619|ref|ZP_11348193.1| RNA polymerase primary sigma factor [Glaciecola lipolytica E3]
 gi|410142812|dbj|GAC15398.1| RNA polymerase primary sigma factor [Glaciecola lipolytica E3]
          Length = 609

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 412/604 (68%), Gaps = 10/604 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D++ L++
Sbjct: 8    QIKLLIVKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPDSDELLM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68   QETTADEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 1004
              +  +++  P  I  +L   D+    EI++ +I+ G +D N        +     +   
Sbjct: 128  NQVQCSVAEYPEAITYLLDQWDQFEAEEIRLSDIIIGFVDPNETDVAPTATHVGSELSEE 187

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            + ++E+    +    +  T    +L  E   KF  +   + K R     +G + +   K 
Sbjct: 188  ELDDEDDDEDDEDEEEEDTGPDPELARE---KFDELRKQYIKARDVIASKGRSHKDARKQ 244

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
             N +S      R   K  +++   +R+ +++V   E+ +++  V    MP+  FIK F  
Sbjct: 245  INELSEVFKEFRLVPKQFDRMVKNMRSMMDRVRVQERIVMKHCVVNAKMPKKDFIKAFAG 304

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE   +W+    +    Y   L      ++    K+  ++ +  L + D++DINR+M  G
Sbjct: 305  NETTTDWLVEVLESGASYVPALIEVREELERAVSKMNQVEEETGLIIADIKDINRRMSIG 364

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 365  EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 424

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M 
Sbjct: 425  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMI 484

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L
Sbjct: 485  MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSATGGSLKDATQEVL 544

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+
Sbjct: 545  AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLR 604

Query: 1425 IFLE 1428
             FL+
Sbjct: 605  SFLD 608



 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 298/591 (50%), Positives = 402/591 (68%), Gaps = 10/591 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D++ L++
Sbjct: 8   QIKLLIVKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIQVFESAPDSDELLM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAKRIE+G+
Sbjct: 68  QETTADEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSNNRVIKGN 214
             +  +++  P  I  +L   D+    EI++ +I+ G +D N        +     +   
Sbjct: 128 NQVQCSVAEYPEAITYLLDQWDQFEAEEIRLSDIIIGFVDPNETDVAPTATHVGSELSEE 187

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           + ++E+    +    +  T    +L  E   KF  +   + K R     +G + +   K 
Sbjct: 188 ELDDEDDDEDDEDEEEEDTGPDPELARE---KFDELRKQYIKARDVIASKGRSHKDARKQ 244

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
            N +S      R   K  +++   +R+ +++V   E+ +++  V    MP+  FIK F  
Sbjct: 245 INELSEVFKEFRLVPKQFDRMVKNMRSMMDRVRVQERIVMKHCVVNAKMPKKDFIKAFAG 304

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NE   +W+    +    Y   L      ++    K+  ++ +  L + D++DINR+M  G
Sbjct: 305 NETTTDWLVEVLESGASYVPALIEVREELERAVSKMNQVEEETGLIIADIKDINRRMSIG 364

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 365 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 424

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ +M 
Sbjct: 425 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMI 484

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S++   +++L
Sbjct: 485 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIVQPLDSATGGSLKDATQEVL 544

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 595


>gi|418362285|ref|ZP_12962924.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
            salmonicida 01-B526]
 gi|356686547|gb|EHI51145.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
            salmonicida 01-B526]
          Length = 616

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/612 (49%), Positives = 415/612 (67%), Gaps = 19/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            +  +  +++  P  I  +L   DK    ++ + +I+ G ID N + +      +  +   
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDIISGFIDPNEADDVAPTATHIGSELG 187

Query: 1011 KILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSES 1060
            +  +     D   +       +             KF ++   ++  R + +K G   E 
Sbjct: 188  EDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSIQKNGRAHED 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
               A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F+ 
Sbjct: 248  TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +  ++D
Sbjct: 308  AFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSIAQIKD 363

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P
Sbjct: 424  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNP 483

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+
Sbjct: 484  EELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESL 543

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 544  RNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 603

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 604  PSRSEVLRSFLD 615



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/599 (49%), Positives = 406/599 (67%), Gaps = 19/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           +  +  +++  P  I  +L   DK    ++ + +I+ G ID N + +      +  +   
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDIISGFIDPNEADDVAPTATHIGSELG 187

Query: 221 KILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSES 270
           +  +     D   +       +             KF ++   ++  R + +K G   E 
Sbjct: 188 EDDLADEDEDEDEDDDGDSSDDEGDGGPDPEVAREKFGDLRAQYEVTRLSIQKNGRAHED 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
              A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F+ 
Sbjct: 248 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPLNDLRD 386
            F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +  ++D
Sbjct: 308 AFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSIAQIKD 363

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P
Sbjct: 424 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNP 483

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+
Sbjct: 484 EELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESL 543

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 RNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|261210089|ref|ZP_05924387.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
 gi|260840854|gb|EEX67396.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC341]
          Length = 628

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 321/632 (50%), Positives = 418/632 (66%), Gaps = 37/632 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 175

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------------------------K 1036
            +      I  E S ADL+ E  E    E                               K
Sbjct: 176  EAPTATHIGSELSEADLADEDDEIAAEEDDEDEDEDENGEGESSDSEEEVGIDPELAREK 235

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 1096
            F+ +   F  ++ A  + G +S    +A   I +     R T K  + L +TLR  +++V
Sbjct: 236  FNELRGKFQNLQLAVNEFGRDSNQASEASGLILDIFREFRLTPKQFDHLVETLRTSMDRV 295

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
               E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+  
Sbjct: 296  RTQERLVMKAVVEIAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVRDQEEDIRRS 355

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
             QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 356  IQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 415

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 416  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 475

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 476  NKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 535

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 536  DFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 595

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  DVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 627



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 314/619 (50%), Positives = 409/619 (66%), Gaps = 37/619 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +++ G +D N           
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMET------- 175

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI----------------------------K 246
           +      I  E S ADL+ E  E    E                               K
Sbjct: 176 EAPTATHIGSELSEADLADEDDEIAAEEDDEDEDEDENGEGESSDSEEEVGIDPELAREK 235

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQV 306
           F+ +   F  ++ A  + G +S    +A   I +     R T K  + L +TLR  +++V
Sbjct: 236 FNELRGKFQNLQLAVNEFGRDSNQASEASGLILDIFREFRLTPKQFDHLVETLRTSMDRV 295

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
              E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+  
Sbjct: 296 RTQERLVMKAVVEIAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVRDQEEDIRRS 355

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
            QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 356 IQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 415

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 416 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 475

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 476 NKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG 535

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 536 DFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 595

Query: 607 DVTRERIRQIEAKALRKLR 625
           DVTRERIRQIEAKALRKLR
Sbjct: 596 DVTRERIRQIEAKALRKLR 614


>gi|145300336|ref|YP_001143177.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
            salmonicida A449]
 gi|142853108|gb|ABO91429.1| RNA polymerase sigma factor RpoD [Aeromonas salmonicida subsp.
            salmonicida A449]
          Length = 616

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/612 (49%), Positives = 415/612 (67%), Gaps = 19/612 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            +  +  +++  P  I  +L   DK    ++ + +I+ G ID N + +      +  +   
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDIISGFIDPNEADDVAPTATHIGSELG 187

Query: 1011 KILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSES 1060
            +  +     D   +       +             KF ++   ++  R + +K G   E 
Sbjct: 188  EDDLADEDEDEDEDDDGDSSDDEGDSGPDPEVAREKFGDLRAQYEVTRLSIQKNGRAHED 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
               A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F+ 
Sbjct: 248  TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +  ++D
Sbjct: 308  AFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSIAQIKD 363

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P
Sbjct: 424  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNP 483

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+
Sbjct: 484  EELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESL 543

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 544  RNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 603

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 604  PSRSEVLRSFLD 615



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/599 (49%), Positives = 406/599 (67%), Gaps = 19/599 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           +  +  +++  P  I  +L   DK    ++ + +I+ G ID N + +      +  +   
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLGLSDIISGFIDPNEADDVAPTATHIGSELG 187

Query: 221 KILIESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSES 270
           +  +     D   +       +             KF ++   ++  R + +K G   E 
Sbjct: 188 EDDLADEDEDEDEDDDGDSSDDEGDSGPDPEVAREKFGDLRAQYEVTRLSIQKNGRAHED 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
              A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+  F+ 
Sbjct: 248 TQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPKKTFVA 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPLNDLRD 386
            F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +  ++D
Sbjct: 308 AFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSIAQIKD 363

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 364 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 423

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+P
Sbjct: 424 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPNP 483

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S+
Sbjct: 484 EELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSESL 543

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 544 RNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|381395833|ref|ZP_09921527.1| RNA polymerase primary sigma factor [Glaciecola punicea DSM 14233 =
            ACAM 611]
 gi|379328398|dbj|GAB56660.1| RNA polymerase primary sigma factor [Glaciecola punicea DSM 14233 =
            ACAM 611]
          Length = 622

 Score =  570 bits (1469), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 308/613 (50%), Positives = 415/613 (67%), Gaps = 10/613 (1%)

Query: 823  REEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH 882
            R  +++ + + K+LI  GKE+GYLTF+E+ND LP +++D + IE II+    M I V E 
Sbjct: 12   RYNVQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPANVVDSDQIEDIIRMINDMGIKVFEQ 71

Query: 883  VLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
              D + L++   T+D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIE
Sbjct: 72   APDADELLMQETTTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIE 131

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEG+  +  +++  P  I  +L   D     EI++ +I+ G ID N    + V  
Sbjct: 132  IAKRIEEGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIIIGFIDPN---EDDVAP 188

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEG 1055
               N   E    + +  +   +  E  + ++ +       KF+ +   +   R   E +G
Sbjct: 189  SATNVGSELADSDRNKDNNDDDDEEDEEVDNSVDPELAREKFAALRVQYGIARDVIESKG 248

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             + ++  K    +S+     R   K  +++   +R  +++V   E+ +++  V    MPR
Sbjct: 249  RSHKAARKEIAALSDVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLVMKYCVINAKMPR 308

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              FIK F  NE +  W+    + + DY   +      I+    K+  ++ +  L + D++
Sbjct: 309  KDFIKAFAGNETSTKWLHKLLEGKQDYVERVLEFKEEIERCVSKMNAVEKETGLVIPDIK 368

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 369  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 428

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 429  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 488

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S
Sbjct: 489  PEELSERMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTITQPLDSATGGS 548

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549  LKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR  +LK FL+
Sbjct: 609  HPSRSEQLKSFLD 621



 Score =  553 bits (1426), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 300/600 (50%), Positives = 405/600 (67%), Gaps = 10/600 (1%)

Query: 33  REEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH 92
           R  +++ + + K+LI  GKE+GYLTF+E+ND LP +++D + IE II+    M I V E 
Sbjct: 12  RYNVQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPANVVDSDQIEDIIRMINDMGIKVFEQ 71

Query: 93  VLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
             D + L++   T+D+D  EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIE
Sbjct: 72  APDADELLMQETTTDEDAAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIE 131

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEG+  +  +++  P  I  +L   D     EI++ +I+ G ID N    + V  
Sbjct: 132 IAKRIEEGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRLSDIIIGFIDPN---EDDVAP 188

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEG 265
              N   E    + +  +   +  E  + ++ +       KF+ +   +   R   E +G
Sbjct: 189 SATNVGSELADSDRNKDNNDDDDEEDEEVDNSVDPELAREKFAALRVQYGIARDVIESKG 248

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            + ++  K    +S+     R   K  +++   +R  +++V   E+ +++  V    MPR
Sbjct: 249 RSHKAARKEIAALSDVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLVMKYCVINAKMPR 308

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             FIK F  NE +  W+    + + DY   +      I+    K+  ++ +  L + D++
Sbjct: 309 KDFIKAFAGNETSTKWLHKLLEGKQDYVERVLEFKEEIERCVSKMNAVEKETGLVIPDIK 368

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 369 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 428

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP 
Sbjct: 429 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPT 488

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S
Sbjct: 489 PEELSERMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTITQPLDSATGGS 548

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 LKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 608


>gi|417950658|ref|ZP_12593776.1| RNA polymerase sigma factor RpoD [Vibrio splendidus ATCC 33789]
 gi|342806120|gb|EGU41358.1| RNA polymerase sigma factor RpoD [Vibrio splendidus ATCC 33789]
          Length = 614

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 310/611 (50%), Positives = 421/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123  KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++   A+   ++ E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183  IGSELAETDLDDEDAEDVDDEAEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S   + A   + +     R T K  + L + LRN +++V   E+ I+   V    MP+  
Sbjct: 243  SPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W+D        Y   + R+   I+   QKL  ++ +  L +  ++DI
Sbjct: 303  FIALFTGNESSEAWLDEVLASDKPYAEKIKRHEGDIRRSIQKLDMIEKETSLTVQSIKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSETLRSFLD 613



 Score =  555 bits (1430), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/598 (50%), Positives = 412/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123 KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++   A+   ++ E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183 IGSELAETDLDDEDAEDVDDEAEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S   + A   + +     R T K  + L + LRN +++V   E+ I+   V    MP+  
Sbjct: 243 SPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W+D        Y   + R+   I+   QKL  ++ +  L +  ++DI
Sbjct: 303 FIALFTGNESSEAWLDEVLASDKPYAEKIKRHEGDIRRSIQKLDMIEKETSLTVQSIKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|254784701|ref|YP_003072129.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
 gi|237686864|gb|ACR14128.1| RNA polymerase sigma factor RpoD [Teredinibacter turnerae T7901]
          Length = 619

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 305/621 (49%), Positives = 418/621 (67%), Gaps = 24/621 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E  + + K LI  G+E+GYLT+ E+ND LP+DI D + +E II+    M I V E   D 
Sbjct: 3    EQQQSRIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDA 62

Query: 887  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L++++   + D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IA
Sbjct: 63   DELLMTDGEASPDEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK----------NF 994
            KRIEEGL++++HA++  P  + +I+   D + K E ++++++ G +D           + 
Sbjct: 123  KRIEEGLRELMHALAFWPNAVQQIMDEYDLVEKEERRLNDVISGWLDPAEEVEAATPVDS 182

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR------ 1048
            + NN      KN+ +++   +    +      ++ +  S I        FD++R      
Sbjct: 183  TDNN-----TKNDADDEDDSDDDEDEDDDSSSDEDENNSGIDPEYARERFDELRVQLVAA 237

Query: 1049 -KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
              A  K G +S+    A   +       +   +  + + + +R+ + ++   EK+I+ + 
Sbjct: 238  NDAIAKHGLDSKETGVALEALGEVFKFFKLAPRQFDPIYNYVRDVLARIRAEEKEIMRLC 297

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V   GMPR  F+K FP NEIN +W+    + + DY+  L      I   Q+KL  ++ + 
Sbjct: 298  VRMAGMPRKTFVKEFPGNEINEDWIPEIIRKKRDYSDSLRPVEGDILRSQRKLQQIEEET 357

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L L  +++INR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 358  GLELTAIKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 417

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 418  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 477

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P
Sbjct: 478  QEMGREPTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTITSP 537

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             ++A +  +    K +L  LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 538  VESATSQGLMEATKAVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 597

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 598  AKALRKLRHPSRSDHLRGFLD 618



 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 298/608 (49%), Positives = 409/608 (67%), Gaps = 24/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E  + + K LI  G+E+GYLT+ E+ND LP+DI D + +E II+    M I V E   D 
Sbjct: 3   EQQQSRIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDA 62

Query: 97  ETLMLSN--ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L++++   + D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IA
Sbjct: 63  DELLMTDGEASPDEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK----------NF 204
           KRIEEGL++++HA++  P  + +I+   D + K E ++++++ G +D           + 
Sbjct: 123 KRIEEGLRELMHALAFWPNAVQQIMDEYDLVEKEERRLNDVISGWLDPAEEVEAATPVDS 182

Query: 205 SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR------ 258
           + NN      KN+ +++   +    +      ++ +  S I        FD++R      
Sbjct: 183 TDNN-----TKNDADDEDDSDDDEDEDDDSSSDEDENNSGIDPEYARERFDELRVQLVAA 237

Query: 259 -KAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
             A  K G +S+    A   +       +   +  + + + +R+ + ++   EK+I+ + 
Sbjct: 238 NDAIAKHGLDSKETGVALEALGEVFKFFKLAPRQFDPIYNYVRDVLARIRAEEKEIMRLC 297

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V   GMPR  F+K FP NEIN +W+    + + DY+  L      I   Q+KL  ++ + 
Sbjct: 298 VRMAGMPRKTFVKEFPGNEINEDWIPEIIRKKRDYSDSLRPVEGDILRSQRKLQQIEEET 357

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L L  +++INR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 358 GLELTAIKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 417

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 418 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 477

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +  +MEMPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P
Sbjct: 478 QEMGREPTPEELGERMEMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTITSP 537

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            ++A +  +    K +L  LT RE+KVLRMRFGIEM++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 538 VESATSQGLMEATKAVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIE 597

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 598 AKALRKLR 605


>gi|336125140|ref|YP_004567188.1| RpoD [Vibrio anguillarum 775]
 gi|335342863|gb|AEH34146.1| RpoD [Vibrio anguillarum 775]
          Length = 618

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 308/615 (50%), Positives = 414/615 (67%), Gaps = 13/615 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDNAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  A++  P TI  IL   DK+   E+++ +++ G +D +  + N     +
Sbjct: 123  KRIEDGINQVQRAVAEYPGTIPYILEQFDKVLAEELRLTDLISGFVDPDSDATNAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 1053
              +      +         +  +    +           +L KF+ +   +  ++ A  +
Sbjct: 183  IGSELASADLADEDDLDDDDDDDSEDTDSEEDAGIDPELALEKFTELRNKYQNLQLAKNE 242

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             GY+S    +A   + +     R T K  + L + LR  +++V   E+ I+   V    M
Sbjct: 243  HGYDSNKAAQATELMLDIFREFRLTPKQFDYLVNKLRTSMDRVRTQERLIMRAAVEYGKM 302

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FI +F  NE +  W+D     +  Y   + +    I+    KL  ++ +  L + +
Sbjct: 303  PKKSFIALFTGNESSDAWLDEVLASEKPYAEKIRQQEEDIRRSIHKLKMIEEETSLNVQN 362

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363  IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483  PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S+R+  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543  TSLRAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 603  LRHPSRSETLRSFLD 617



 Score =  555 bits (1430), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 301/602 (50%), Positives = 405/602 (67%), Gaps = 13/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDNAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  A++  P TI  IL   DK+   E+++ +++ G +D +  + N     +
Sbjct: 123 KRIEDGINQVQRAVAEYPGTIPYILEQFDKVLAEELRLTDLISGFVDPDSDATNAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 263
             +      +         +  +    +           +L KF+ +   +  ++ A  +
Sbjct: 183 IGSELASADLADEDDLDDDDDDDSEDTDSEEDAGIDPELALEKFTELRNKYQNLQLAKNE 242

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            GY+S    +A   + +     R T K  + L + LR  +++V   E+ I+   V    M
Sbjct: 243 HGYDSNKAAQATELMLDIFREFRLTPKQFDYLVNKLRTSMDRVRTQERLIMRAAVEYGKM 302

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FI +F  NE +  W+D     +  Y   + +    I+    KL  ++ +  L + +
Sbjct: 303 PKKSFIALFTGNESSDAWLDEVLASEKPYAEKIRQQEEDIRRSIHKLKMIEEETSLNVQN 362

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S+R+  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543 TSLRAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 624 LR 625
           LR
Sbjct: 603 LR 604


>gi|386390298|ref|ZP_10075089.1| RNA polymerase sigma factor RpoD [Haemophilus paraphrohaemolyticus
            HK411]
 gi|385693333|gb|EIG23982.1| RNA polymerase sigma factor RpoD [Haemophilus paraphrohaemolyticus
            HK411]
          Length = 624

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/616 (49%), Positives = 411/616 (66%), Gaps = 21/616 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12   QSRIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72   MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK--- 1005
            EG+ ++  A++  P  +  +L    ++    +++ +++   +D N    N V   +    
Sbjct: 131  EGINEVQCAVAEYPEALEGVLSCYAEVEAGNMRLVDLITAFVDPNAQEENPVADDDSIHL 190

Query: 1006 NNNEEKILIE-----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFE 1052
            ++NE   + +           S +AD   +     +L  E   KF+ +   ++    A  
Sbjct: 191  DDNEHADVDDVEDEEEEEDGDSGNADSGDDNSIDPELARE---KFTALKEQYENALLAIR 247

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            K G       +  N +S+     R   K  + L +T++  + QV   E+QI    V   G
Sbjct: 248  KHGRTHAKAREQINALSDIFREFRLVPKQFDLLVETMQKLMKQVRSEERQIQRYAVEYAG 307

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            M +  F+K F  NE +  W++     +      L   +  I+     L NL+ +  L + 
Sbjct: 308  MKKADFLKNFQGNETSEAWMEKAINAKRGGVPKLANYVEKIRVNITNLQNLEQNSGLTIT 367

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
             +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 368  QIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 427

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G 
Sbjct: 428  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGR 487

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A 
Sbjct: 488  EATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSAT 547

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 548  AESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 607

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FL+
Sbjct: 608  KLRHPSRSETLRSFLD 623



 Score =  555 bits (1429), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 300/603 (49%), Positives = 402/603 (66%), Gaps = 21/603 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12  QSRIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIQVLETAPDTDEL 71

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NIT +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72  MLAENITDEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREDEIQISKRIE 130

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK--- 215
           EG+ ++  A++  P  +  +L    ++    +++ +++   +D N    N V   +    
Sbjct: 131 EGINEVQCAVAEYPEALEGVLSCYAEVEAGNMRLVDLITAFVDPNAQEENPVADDDSIHL 190

Query: 216 NNNEEKILIE-----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFE 262
           ++NE   + +           S +AD   +     +L  E   KF+ +   ++    A  
Sbjct: 191 DDNEHADVDDVEDEEEEEDGDSGNADSGDDNSIDPELARE---KFTALKEQYENALLAIR 247

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           K G       +  N +S+     R   K  + L +T++  + QV   E+QI    V   G
Sbjct: 248 KHGRTHAKAREQINALSDIFREFRLVPKQFDLLVETMQKLMKQVRSEERQIQRYAVEYAG 307

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           M +  F+K F  NE +  W++     +      L   +  I+     L NL+ +  L + 
Sbjct: 308 MKKADFLKNFQGNETSEAWMEKAINAKRGGVPKLANYVEKIRVNITNLQNLEQNSGLTIT 367

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
            +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 368 QIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 427

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G 
Sbjct: 428 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGR 487

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A 
Sbjct: 488 EATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSAT 547

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 548 AESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 607

Query: 623 KLR 625
           KLR
Sbjct: 608 KLR 610


>gi|411010639|ref|ZP_11386968.1| RNA polymerase sigma factor RpoD [Aeromonas aquariorum AAK1]
 gi|423199785|ref|ZP_17186367.1| RNA polymerase sigma factor rpoD [Aeromonas hydrophila SSU]
 gi|404628863|gb|EKB25634.1| RNA polymerase sigma factor rpoD [Aeromonas hydrophila SSU]
          Length = 618

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/613 (49%), Positives = 414/613 (67%), Gaps = 19/613 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 995
            +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETDDVAPTATHIGSELS 187

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
              +   +    + +E    + S  D       ++  E   KF  +   ++  R + ++ G
Sbjct: 188  EEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQQNG 244

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245  RAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
              F+  F  NE    W + + +    ++  L      +     KL  ++ +  L +  ++
Sbjct: 305  KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDVLRAIGKLQQIEEETGLSIAQIK 364

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365  DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+
Sbjct: 425  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPN 484

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S
Sbjct: 485  PEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSES 544

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            +R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545  LRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FL+
Sbjct: 605  HPSRSEVLRSFLD 617



 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 295/600 (49%), Positives = 405/600 (67%), Gaps = 19/600 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 205
           +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNETDDVAPTATHIGSELS 187

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
             +   +    + +E    + S  D       ++  E   KF  +   ++  R + ++ G
Sbjct: 188 EEDLADEDEDEDEDEDGDGDDSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQQNG 244

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              E    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245 RAHEDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
             F+  F  NE    W + + +    ++  L      +     KL  ++ +  L +  ++
Sbjct: 305 KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEDVLRAIGKLQQIEEETGLSIAQIK 364

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 365 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 424

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP+
Sbjct: 425 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPN 484

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA + S
Sbjct: 485 PEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAATSES 544

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 LRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|295698766|ref|YP_003603421.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
            USDA]
 gi|291157279|gb|ADD79724.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
            USDA]
          Length = 629

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 319/634 (50%), Positives = 423/634 (66%), Gaps = 43/634 (6%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+T   M I V+E V D +
Sbjct: 4    NPKSQLKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDED 63

Query: 888  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
             L+L++ TS  D EE  EAA   LS+V+ + GRT DPI+MYMREMG++ELLTR+GEI+IA
Sbjct: 64   ELILTDPTSSTD-EETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL-----------IDKN 993
            KRIE+G+  +  +IS  P +I  IL         E+K+ +I+ GL           +DKN
Sbjct: 123  KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDIITGLSSEDTFSSSKNVDKN 182

Query: 994  FSSN-----NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE----SLIKFSNISFHF 1044
            FSS      N V+    +NN EK  I  S     T   ++  +     +  KF  +   +
Sbjct: 183  FSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDPKIARKKFLELQNQY 242

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +K+  + ++ G  S   I    ++       R   K ++ L   +R  I ++   EK I+
Sbjct: 243  EKVTHSLKENGIKSSQSILDIQDLCEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLII 302

Query: 1105 EIVVNKCGMPRLHFIKVFPEN--EINLNWV--------DNETKIQHDYNLILCRNIPSIK 1154
             I   +  +P+ +F+ +F EN  E +L  +         +E K + D  ++   N     
Sbjct: 303  NISFKEYKIPKKYFLNLFSENPKEYDLKELIVSNRYNKKDEKKFKLDSTIVQALN----- 357

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
                +L  ++ D  + ++ +++I RK+  GE  AR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 358  ----ELNEIEKDTGISISKIKEIGRKISIGETIARRAKKEMVEANLRLVISIAKKYTNRG 413

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 414  LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 473

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++ ISRQILQETG EP P  ++ +M +PEEKIRK++KIA+EP+SME+P+GDDEDSH
Sbjct: 474  TINKLNHISRQILQETGREPSPEELSERMLIPEEKIRKVLKIAREPISMETPIGDDEDSH 533

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED  +  P ++A + S+RS   ++L+ LT RE+KVLRMRFGI+M +DHTLEEVGK
Sbjct: 534  LGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGK 593

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            QFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 594  QFDVTRERIRQIEAKALRKLRHPSRSELLRSFLD 627



 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 312/621 (50%), Positives = 414/621 (66%), Gaps = 43/621 (6%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+T   M I V+E V D +
Sbjct: 4   NPKSQLKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDED 63

Query: 98  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
            L+L++ TS  D EE  EAA   LS+V+ + GRT DPI+MYMREMG++ELLTR+GEI+IA
Sbjct: 64  ELILTDPTSSTD-EETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL-----------IDKN 203
           KRIE+G+  +  +IS  P +I  IL         E+K+ +I+ GL           +DKN
Sbjct: 123 KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDIITGLSSEDTFSSSKNVDKN 182

Query: 204 FSSN-----NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE----SLIKFSNISFHF 254
           FSS      N V+    +NN EK  I  S     T   ++  +     +  KF  +   +
Sbjct: 183 FSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDPKIARKKFLELQNQY 242

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +K+  + ++ G  S   I    ++       R   K ++ L   +R  I ++   EK I+
Sbjct: 243 EKVTHSLKENGIKSSQSILDIQDLCEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLII 302

Query: 315 EIVVNKCGMPRLHFIKVFPEN--EINLNWV--------DNETKIQHDYNLILCRNIPSIK 364
            I   +  +P+ +F+ +F EN  E +L  +         +E K + D  ++   N     
Sbjct: 303 NISFKEYKIPKKYFLNLFSENPKEYDLKELIVSNRYNKKDEKKFKLDSTIVQALN----- 357

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
               +L  ++ D  + ++ +++I RK+  GE  AR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 358 ----ELNEIEKDTGISISKIKEIGRKISIGETIARRAKKEMVEANLRLVISIAKKYTNRG 413

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 414 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 473

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++ ISRQILQETG EP P  ++ +M +PEEKIRK++KIA+EP+SME+P+GDDEDSH
Sbjct: 474 TINKLNHISRQILQETGREPSPEELSERMLIPEEKIRKVLKIAREPISMETPIGDDEDSH 533

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED  +  P ++A + S+RS   ++L+ LT RE+KVLRMRFGI+M +DHTLEEVGK
Sbjct: 534 LGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGK 593

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKALRKLR
Sbjct: 594 QFDVTRERIRQIEAKALRKLR 614


>gi|372268985|ref|ZP_09505033.1| RNA polymerase sigma factor RpoD [Alteromonas sp. S89]
          Length = 618

 Score =  570 bits (1468), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 304/605 (50%), Positives = 404/605 (66%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + + LI  GKE+GYLT++E+ND LPEDI D + +E II     M I V E   D E L++
Sbjct: 13   RIRELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIGMINDMGIKVFEQAPDAEELLM 72

Query: 892  SNITSDDDVEEATEAALSTVD--SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            +   S  D   A EAA +     SD GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 73   AEGDSSADEIAAAEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 132

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGN 1004
            GL++++ A++  P  +  I+     I K E +I +++ G +D        +   +  + +
Sbjct: 133  GLRELMAALAYWPGAVQHIIDEYALIEKEERRIPDVIAGWLDPAEDVPPGAQAGQAAQAS 192

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK-MRKAFEKEGYNSESYIK 1063
            K  + +    +   ++   E +  +  E L +  N      K    A +K G +S+    
Sbjct: 193  KEEDSDDDSDDDDDSEEEEENVGGIDPEELAERMNALIAAQKKADAAIKKHGRDSKEAGT 252

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   +       +   +  + L   +RN +++V   E+ ++ + + +  MPR  FIK FP
Sbjct: 253  AMEAVGEVFRFFKLAPRQFDPLYTEVRNILDEVRAQERLVMNLCIKRARMPRKTFIKEFP 312

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE N +W+    K + DY+  L +    I+  Q+KL   Q    L +  +++INR+M  
Sbjct: 313  GNETNQDWIPAIIKKKRDYSDALRQVADEIQRAQRKLQQAQEKAQLDVGQIKEINRRMSI 372

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE ++R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 373  GEARSRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 432

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 433  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 492

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
            +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N  +P D A +  +    + +
Sbjct: 493  DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNQSSPVDTATSTGLHDATRSV 552

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 553  LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEHL 612

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 613  RSFLD 617



 Score =  555 bits (1429), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/592 (50%), Positives = 395/592 (66%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + + LI  GKE+GYLT++E+ND LPEDI D + +E II     M I V E   D E L++
Sbjct: 13  RIRELIARGKEQGYLTYAEVNDHLPEDISDPDQVEDIIGMINDMGIKVFEQAPDAEELLM 72

Query: 102 SNITSDDDVEEATEAALSTVD--SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           +   S  D   A EAA +     SD GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 73  AEGDSSADEIAAAEAAAALAAVESDVGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 132

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-----FSSNNRVIKGN 214
           GL++++ A++  P  +  I+     I K E +I +++ G +D        +   +  + +
Sbjct: 133 GLRELMAALAYWPGAVQHIIDEYALIEKEERRIPDVIAGWLDPAEDVPPGAQAGQAAQAS 192

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDK-MRKAFEKEGYNSESYIK 273
           K  + +    +   ++   E +  +  E L +  N      K    A +K G +S+    
Sbjct: 193 KEEDSDDDSDDDDDSEEEEENVGGIDPEELAERMNALIAAQKKADAAIKKHGRDSKEAGT 252

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   +       +   +  + L   +RN +++V   E+ ++ + + +  MPR  FIK FP
Sbjct: 253 AMEAVGEVFRFFKLAPRQFDPLYTEVRNILDEVRAQERLVMNLCIKRARMPRKTFIKEFP 312

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE N +W+    K + DY+  L +    I+  Q+KL   Q    L +  +++INR+M  
Sbjct: 313 GNETNQDWIPAIIKKKRDYSDALRQVADEIQRAQRKLQQAQEKAQLDVGQIKEINRRMSI 372

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE ++R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 373 GEARSRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 432

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M
Sbjct: 433 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERM 492

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
           +MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N  +P D A +  +    + +
Sbjct: 493 DMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNQSSPVDTATSTGLHDATRSV 552

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 553 LGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|416894492|ref|ZP_11925080.1| RNA polymerase sigma factor RpoD [Aggregatibacter aphrophilus ATCC
            33389]
 gi|347813454|gb|EGY30127.1| RNA polymerase sigma factor RpoD [Aggregatibacter aphrophilus ATCC
            33389]
          Length = 623

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 299/625 (47%), Positives = 411/625 (65%), Gaps = 30/625 (4%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4    NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
             LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64   DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 1005
            EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124  EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 1043
            +++EE      +  D+   +L+    +                         KF+ +   
Sbjct: 184  DSDEE------NEEDVGDNRLDDESEDEEDREENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
              K   + EK G  S+        +S+     R   K  + L  ++R+ + ++   E+ I
Sbjct: 238  HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDIMKRMRAQERFI 297

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
              IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298  QRIVVDNAKMPKSSFQKSFIGHETTDTWLIKALGAGKAWSEKLVQYENDLRQAIANLVQI 357

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358  EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478  RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538  LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 598  RQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 292/612 (47%), Positives = 402/612 (65%), Gaps = 30/612 (4%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLT++E+ND LPE+++D + IE II+    M I V E   D +
Sbjct: 4   NPQSQLKLLIAQGKEQGYLTYAEVNDSLPEELVDADQIEDIIQMINDMGIQVLETAPDAD 63

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
            LML+   +D+DV E     LS+V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRI
Sbjct: 64  DLMLNETITDEDVVEEATQVLSSVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRI 123

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF--SSNNRVIKGNK 215
           EEG+ ++  A+++ P  I  ++   + +    +++ +++ G +D N    S+N  +  N 
Sbjct: 124 EEGINEVQSAVAAYPEAITYLIEQYESVENGGVRLADLITGFVDPNVLSESDNTHLDENF 183

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYESLI----------------------KFSNISFH 253
           +++EE      +  D+   +L+    +                         KF+ +   
Sbjct: 184 DSDEE------NEEDVGDNRLDDESEDEEDREENSSDDGDSDNSIDPEVAREKFTALKEQ 237

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
             K   + EK G  S+        +S+     R   K  + L  ++R+ + ++   E+ I
Sbjct: 238 HQKTLASIEKHGRTSKKTKDEIQALSDIFTQFRLVPKQFDILVLSMRDIMKRMRAQERFI 297

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
             IVV+   MP+  F K F  +E    W+         ++  L +    +++    L+ +
Sbjct: 298 QRIVVDNAKMPKSSFQKSFIGHETTDTWLIKALGAGKAWSEKLVQYENDLRQAIANLVQI 357

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + D  L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 358 EQDTHLTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 418 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 477

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 478 RQMLQEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 537

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 538 LELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 597

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 598 RQIEAKALRKLR 609


>gi|359430820|ref|ZP_09221804.1| RNA polymerase sigma factor RpoD [Acinetobacter sp. NBRC 100985]
 gi|358233713|dbj|GAB03343.1| RNA polymerase sigma factor RpoD [Acinetobacter sp. NBRC 100985]
          Length = 628

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/617 (49%), Positives = 417/617 (67%), Gaps = 28/617 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------------------K 992
            ++H+I+  P  +  +L   +     E ++ +I+ G +D                     +
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEEESEEIEEDE 193

Query: 993  NFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 1052
              SS  + +K + ++ EE+   +  S   S    E  K    ++FS +   +++ +    
Sbjct: 194  KASSKTKDVKLDDDDEEEESESDDDSEGDSGPDPEVAK----VRFSELEAAWNETKTVIA 249

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            K G NS+    A   ++   +  +FT +  E + + +R   +Q+   E++I+   V +  
Sbjct: 250  KHGRNSDEAKAALEALAAVFMMFKFTPRLFEIISEMIRGTHDQIRSNEREIMRYAVRRGR 309

Query: 1113 MPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
            M R  F   FPE E NL W+D +  K   +    L +  P +   QQK+ +++ D+ L +
Sbjct: 310  MDRTQFRTTFPEQESNLAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNV 369

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
             D++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 370  KDIKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 429

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G
Sbjct: 430  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMG 489

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA
Sbjct: 490  REPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAA 549

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 550  TSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKAL 609

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FLE
Sbjct: 610  RKLRHPSRSEHLRSFLE 626



 Score =  553 bits (1425), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 299/604 (49%), Positives = 408/604 (67%), Gaps = 28/604 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------------------K 202
           ++H+I+  P  +  +L   +     E ++ +I+ G +D                     +
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEEESEEIEEDE 193

Query: 203 NFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFE 262
             SS  + +K + ++ EE+   +  S   S    E  K    ++FS +   +++ +    
Sbjct: 194 KASSKTKDVKLDDDDEEEESESDDDSEGDSGPDPEVAK----VRFSELEAAWNETKTVIA 249

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           K G NS+    A   ++   +  +FT +  E + + +R   +Q+   E++I+   V +  
Sbjct: 250 KHGRNSDEAKAALEALAAVFMMFKFTPRLFEIISEMIRGTHDQIRSNEREIMRYAVRRGR 309

Query: 323 MPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
           M R  F   FPE E NL W+D +  K   +    L +  P +   QQK+ +++ D+ L +
Sbjct: 310 MDRTQFRTTFPEQESNLAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNV 369

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            D++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 370 KDIKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 429

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G
Sbjct: 430 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMG 489

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA
Sbjct: 490 REPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAA 549

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 550 TSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKAL 609

Query: 622 RKLR 625
           RKLR
Sbjct: 610 RKLR 613


>gi|421498803|ref|ZP_15945884.1| RNA polymerase sigma factor RpoD [Aeromonas media WS]
 gi|407182190|gb|EKE56166.1| RNA polymerase sigma factor RpoD [Aeromonas media WS]
          Length = 618

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/617 (49%), Positives = 420/617 (68%), Gaps = 27/617 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 995
            +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNEADDVAPTATHIGSELS 187

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
             ++   +    + +E    +SS  D       ++  E   KF  +   ++  R + +K G
Sbjct: 188  EDDLADEDEDEDEDEDEDGDSSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQKNG 244

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               +    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245  RAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPL 1171
              F+  F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +
Sbjct: 305  KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEEVLRSIGKLQQ----IEEETGLSI 360

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361  AQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP+P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA
Sbjct: 481  REPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAA 540

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541  TSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 601  RKLRHPSRSEVLRSFLD 617



 Score =  555 bits (1430), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 299/604 (49%), Positives = 411/604 (68%), Gaps = 27/604 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 205
           +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNEADDVAPTATHIGSELS 187

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
            ++   +    + +E    +SS  D       ++  E   KF  +   ++  R + +K G
Sbjct: 188 EDDLADEDEDEDEDEDEDGDSSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQKNG 244

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              +    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245 RAHDDTQAAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPL 381
             F+  F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +
Sbjct: 305 KTFVAAFTNNECETAWFEYQKQAGKAWSPRLVEMDEEVLRSIGKLQQ----IEEETGLSI 360

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361 AQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP+P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA
Sbjct: 481 REPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAA 540

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541 TSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 622 RKLR 625
           RKLR
Sbjct: 601 RKLR 604


>gi|365538639|ref|ZP_09363814.1| RNA polymerase sigma factor RpoD [Vibrio ordalii ATCC 33509]
          Length = 618

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 311/615 (50%), Positives = 417/615 (67%), Gaps = 13/615 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDNAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  A++  P TI  IL   DK+   E+++ +++ G +D +  + N     +
Sbjct: 123  KRIEDGINQVQRAVAEYPGTIPYILEQFDKVLAEELRLTDLISGFVDPDSDATNAPTATH 182

Query: 1005 KNNN----------EEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEK 1053
              +           +     +  S D  +E+   +  E +L KF+ +   +  ++ A  +
Sbjct: 183  IGSELASADLADEDDLDDDEDGDSEDTDSEEETGIDPELALEKFTELRNKYQNLQLAKNE 242

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             GY S    +A   + +     R T K  + L + L   +++V   E+ I+   V    M
Sbjct: 243  HGYESNKAAQATELMLDIFREFRLTPKQFDYLVNKLSTSMDRVRTQERLIMRAAVEYGKM 302

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FI +F  NE +  W+D     +  Y   + +    I+    KL  ++ +  L + +
Sbjct: 303  PKKSFIALFTGNESSDAWLDEVIASEKPYAEKIRQQEEDIRRSIHKLKMIEEETSLNVQN 362

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363  IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483  PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S+R+  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543  TSLRAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 603  LRHPSRSETLRSFLD 617



 Score =  555 bits (1429), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 304/602 (50%), Positives = 408/602 (67%), Gaps = 13/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   N  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDNAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  A++  P TI  IL   DK+   E+++ +++ G +D +  + N     +
Sbjct: 123 KRIEDGINQVQRAVAEYPGTIPYILEQFDKVLAEELRLTDLISGFVDPDSDATNAPTATH 182

Query: 215 KNNN----------EEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEK 263
             +           +     +  S D  +E+   +  E +L KF+ +   +  ++ A  +
Sbjct: 183 IGSELASADLADEDDLDDDEDGDSEDTDSEEETGIDPELALEKFTELRNKYQNLQLAKNE 242

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            GY S    +A   + +     R T K  + L + L   +++V   E+ I+   V    M
Sbjct: 243 HGYESNKAAQATELMLDIFREFRLTPKQFDYLVNKLSTSMDRVRTQERLIMRAAVEYGKM 302

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FI +F  NE +  W+D     +  Y   + +    I+    KL  ++ +  L + +
Sbjct: 303 PKKSFIALFTGNESSDAWLDEVIASEKPYAEKIRQQEEDIRRSIHKLKMIEEETSLNVQN 362

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S+R+  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543 TSLRAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 624 LR 625
           LR
Sbjct: 603 LR 604


>gi|149910043|ref|ZP_01898691.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149806911|gb|EDM66872.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 609

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 301/611 (49%), Positives = 414/611 (67%), Gaps = 11/611 (1%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +E+ + + K+L+  GKE+GYLT++E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 1    MESPQSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQVEDIIQMINDMGIQVLETAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
             + L+++  T+  D + A  AA +  +V+S+ GRT DP++MYMREMG+VELLTR+GEI I
Sbjct: 61   ADDLLMAENTTAPDDDAAEAAAAALASVESEIGRTTDPVRMYMREMGTVELLTREGEIVI 120

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-----SSNN 998
            AKRIEEG+  +  A++  P  I  +L   DK    E ++ +I+ G ID N      ++ +
Sbjct: 121  AKRIEEGIYAVQTAVAEYPEAINSLLAEYDKFLAEESRLSDIITGFIDPNADDVAPTATH 180

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
               +  K  NE     +    +   +  +    E+  KF+ +  H   + K  +  G + 
Sbjct: 181  IGSEVTKKQNESDSTDDDEEEEEGNKGPDP--EEAAEKFAELRKHHTALLKGIKDHGLDH 238

Query: 1059 ESYIKAHNNISNEML-GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
                + H  + +E+    R   K  +++ +++R+ ++ V   E+ ++++ V +C MP+  
Sbjct: 239  PK-TRLHVEMLSEVFRTFRLIPKQFDRIVNSMRDMMDHVRVQERLVIKMCVEQCKMPKAA 297

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F++ F  NE +  W +   +    Y   L R    ++    KL  ++    L ++ +++I
Sbjct: 298  FVEAFAGNETDFTWFEKAQQSAAPYAPALQRIDFDVRRCINKLKLVENTTGLTISQIKNI 357

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 358  NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 417

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P 
Sbjct: 418  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPE 477

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE++IRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   S++
Sbjct: 478  ELAERMMMPEDRIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPVDAATKDSLK 537

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
                D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 538  GATDDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 597

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 598  SRSEQLRSFLD 608



 Score =  553 bits (1426), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 294/598 (49%), Positives = 404/598 (67%), Gaps = 11/598 (1%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +E+ + + K+L+  GKE+GYLT++E+ND LP+DI+D + +E II+    M I V E   D
Sbjct: 1   MESPQSQLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQVEDIIQMINDMGIQVLETAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            + L+++  T+  D + A  AA +  +V+S+ GRT DP++MYMREMG+VELLTR+GEI I
Sbjct: 61  ADDLLMAENTTAPDDDAAEAAAAALASVESEIGRTTDPVRMYMREMGTVELLTREGEIVI 120

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-----SSNN 208
           AKRIEEG+  +  A++  P  I  +L   DK    E ++ +I+ G ID N      ++ +
Sbjct: 121 AKRIEEGIYAVQTAVAEYPEAINSLLAEYDKFLAEESRLSDIITGFIDPNADDVAPTATH 180

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
              +  K  NE     +    +   +  +    E+  KF+ +  H   + K  +  G + 
Sbjct: 181 IGSEVTKKQNESDSTDDDEEEEEGNKGPDP--EEAAEKFAELRKHHTALLKGIKDHGLDH 238

Query: 269 ESYIKAHNNISNEML-GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
               + H  + +E+    R   K  +++ +++R+ ++ V   E+ ++++ V +C MP+  
Sbjct: 239 PK-TRLHVEMLSEVFRTFRLIPKQFDRIVNSMRDMMDHVRVQERLVIKMCVEQCKMPKAA 297

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F++ F  NE +  W +   +    Y   L R    ++    KL  ++    L ++ +++I
Sbjct: 298 FVEAFAGNETDFTWFEKAQQSAAPYAPALQRIDFDVRRCINKLKLVENTTGLTISQIKNI 357

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           NR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 358 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 417

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P 
Sbjct: 418 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREATPE 477

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE++IRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P DAA   S++
Sbjct: 478 ELAERMMMPEDRIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLSLPVDAATKDSLK 537

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 538 GATDDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 595


>gi|260912696|ref|ZP_05919182.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella dagmatis
            ATCC 43325]
 gi|260633074|gb|EEX51239.1| DNA-directed RNA polymerase sigma subunit RpoD [Pasteurella dagmatis
            ATCC 43325]
          Length = 623

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 305/621 (49%), Positives = 414/621 (66%), Gaps = 20/621 (3%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLETAPDA 62

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + LMLS  IT +D VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63   DDLMLSETITDEDAVEEATQV-LSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+ ++  A++  P  +  +L     +    +++ +++ G +D N  +   V + ++
Sbjct: 122  RIEEGINEVQSAVAFYPEALNYLLEQYSLVEDGGVRLADLITGFVDPNAITEEDVAEIDE 181

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKYE------------------SLIKFSNISFHFDKM 1047
            + +E++       A L   + E+ + E                  +  KF  +     K 
Sbjct: 182  SFDEDEDSDTVVGAKLDDTEEEEEESEEENTSDDNDSDNSIDPELAHAKFLELKTQHVKT 241

Query: 1048 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
             +   K G  S+        +++     R   K  + L + +   +  V   E+ I +IV
Sbjct: 242  LETIVKHGRASKKSKDQIQALADVFTQFRLVPKQFDMLVNLMSGMMKSVRLQERNIQKIV 301

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
            V+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++   
Sbjct: 302  VDKAKMPKEQFQKVFIGHENQDTWLVKALSAGKTWSEKLAKHEAEIRASIDNILEIERQT 361

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L +  +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 362  NLTVQQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 421

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 422  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 481

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P
Sbjct: 482  QEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELP 541

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 542  LDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 601

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FL+
Sbjct: 602  AKALRKLRHPSRSETLRSFLD 622



 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 298/608 (49%), Positives = 405/608 (66%), Gaps = 20/608 (3%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+LI  GKE+GYLT++E+ND LPE+++D E IE II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLIAQGKEQGYLTYAEVNDHLPEELVDAEQIEDIIQMINDMGIQVLETAPDA 62

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + LMLS  IT +D VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELLTR+GEI+IAK
Sbjct: 63  DDLMLSETITDEDAVEEATQV-LSSVESEIGRTTDPVRMYMREMGSVELLTREGEIDIAK 121

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+ ++  A++  P  +  +L     +    +++ +++ G +D N  +   V + ++
Sbjct: 122 RIEEGINEVQSAVAFYPEALNYLLEQYSLVEDGGVRLADLITGFVDPNAITEEDVAEIDE 181

Query: 216 NNNEEKILIESSSADLSTEQLEKLKYE------------------SLIKFSNISFHFDKM 257
           + +E++       A L   + E+ + E                  +  KF  +     K 
Sbjct: 182 SFDEDEDSDTVVGAKLDDTEEEEEESEEENTSDDNDSDNSIDPELAHAKFLELKTQHVKT 241

Query: 258 RKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
            +   K G  S+        +++     R   K  + L + +   +  V   E+ I +IV
Sbjct: 242 LETIVKHGRASKKSKDQIQALADVFTQFRLVPKQFDMLVNLMSGMMKSVRLQERNIQKIV 301

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
           V+K  MP+  F KVF  +E    W+         ++  L ++   I+     ++ ++   
Sbjct: 302 VDKAKMPKEQFQKVFIGHENQDTWLVKALSAGKTWSEKLAKHEAEIRASIDNILEIERQT 361

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L +  +R++  ++ AGE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 362 NLTVQQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 421

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+L
Sbjct: 422 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQML 481

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P
Sbjct: 482 QEMGREASPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELP 541

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            D+A   S+++   ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIE
Sbjct: 542 LDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 601

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 602 AKALRKLR 609


>gi|410664489|ref|YP_006916860.1| transcription initiation factor sigma 70 [Simiduia agarivorans SA1 =
            DSM 21679]
 gi|409026846|gb|AFU99130.1| transcription initiation factor sigma 70 [Simiduia agarivorans SA1 =
            DSM 21679]
          Length = 621

 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/610 (49%), Positives = 408/610 (66%), Gaps = 13/610 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V E   D +TL++
Sbjct: 11   RIKELIARGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIKVFETAPDADTLLM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            ++  S  D   A EAA +    +   GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 71   TDGDSSADEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 130

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNK 1005
            G+++++H+++  P  + ++L   + + K E ++ +++ G +D       ++    ++   
Sbjct: 131  GIRELMHSLAYWPGAVKQLLDEYELVEKEERRLVDVIAGWLDPADEVPTAAEQAQMREEA 190

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             N            D      +           E+  +F+ +     K  K+  K G   
Sbjct: 191  ANANNDDDDSDDDDDDDDSSSDDDSNDGGVDPEEARQRFAALRDAHVKYEKSLAKNGRAH 250

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +S  KA N++       +   +  + L   +R  +++V   E+ ++ + V   GMPR  F
Sbjct: 251  KSTDKALNDMGEIFKYFKLPPRQFDPLYGRVRGMLDRVRAEERSVMSLCVRTAGMPRKTF 310

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            IK FP  E N +WV +  K + DY+  L    P I   Q+KL  ++ +  L L  +++IN
Sbjct: 311  IKEFPGMETNDSWVADIIKKKRDYSDALAAVEPEIVRSQRKLQQIEQESELDLASIKEIN 370

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371  RRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 431  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 490

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A    +  
Sbjct: 491  LGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTITSPVESATVEGLIE 550

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 551  ATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 611  RSDHLRSFLD 620



 Score =  555 bits (1429), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 296/597 (49%), Positives = 399/597 (66%), Gaps = 13/597 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT+SE+ND LPEDI D + +E II+    M I V E   D +TL++
Sbjct: 11  RIKELIARGKEQGYLTYSEVNDHLPEDISDPDQVEDIIQMINDMGIKVFETAPDADTLLM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           ++  S  D   A EAA +    +   GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 71  TDGDSSADEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 130

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----FSSNNRVIKGNK 215
           G+++++H+++  P  + ++L   + + K E ++ +++ G +D       ++    ++   
Sbjct: 131 GIRELMHSLAYWPGAVKQLLDEYELVEKEERRLVDVIAGWLDPADEVPTAAEQAQMREEA 190

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNS 268
            N            D      +           E+  +F+ +     K  K+  K G   
Sbjct: 191 ANANNDDDDSDDDDDDDDSSSDDDSNDGGVDPEEARQRFAALRDAHVKYEKSLAKNGRAH 250

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +S  KA N++       +   +  + L   +R  +++V   E+ ++ + V   GMPR  F
Sbjct: 251 KSTDKALNDMGEIFKYFKLPPRQFDPLYGRVRGMLDRVRAEERSVMSLCVRTAGMPRKTF 310

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           IK FP  E N +WV +  K + DY+  L    P I   Q+KL  ++ +  L L  +++IN
Sbjct: 311 IKEFPGMETNDSWVADIIKKKRDYSDALAAVEPEIVRSQRKLQQIEQESELDLASIKEIN 370

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 371 RRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 430

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  
Sbjct: 431 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEE 490

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A    +  
Sbjct: 491 LGERMDMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTITSPVESATVEGLIE 550

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 ATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 607


>gi|357403480|ref|YP_004915404.1| sigma D (sigma 70) factor of RNA polymerase [Methylomicrobium
            alcaliphilum 20Z]
 gi|351716145|emb|CCE21796.1| sigma D (sigma 70) factor of RNA polymerase [Methylomicrobium
            alcaliphilum 20Z]
          Length = 603

 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 302/599 (50%), Positives = 403/599 (67%), Gaps = 12/599 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  GK +GYLT++E+ND LP DI D E IE II     M I V E   D ++L+     
Sbjct: 13   LIAKGKAQGYLTYAEVNDHLPSDIADPEQIEDIIGMINDMGIQVYEDAPDEDSLITDGAA 72

Query: 896  -SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             + D+ ++   AAL++VDS+FGRT DP++MYMREMGSVELL R+ E++IAKRIEEG + +
Sbjct: 73   VTGDEDDDDEVAALASVDSEFGRTTDPVRMYMREMGSVELLNREDELKIAKRIEEGQQQV 132

Query: 955  IHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKI 1012
            + AIS     + E +   D IS  E  I++ ++V G +D   S    V      N++   
Sbjct: 133  VRAISRSCKVVDEFIRDFDSISDEEGGIRLTDLVSGFVD--LSEPETVFSSQAANDD--- 187

Query: 1013 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDK-MRKAFEKEGYNSESYIKAHNNISNE 1071
               S   D   ++++ L Y  + +   +     K    A +K GY      +  + ++  
Sbjct: 188  ---SVDEDADEDEVKGLDYNDVKEKVEVLRKLHKSAAAAIKKHGYGDPKVNEKLDELAES 244

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
             +  ++  +  ++L  T+   +  + + E+ I ++ VN+  M R  FI     +E +  W
Sbjct: 245  FIEFKWAPQYFKRLTATVSEAVALIREKERLIADLCVNEAKMTRKEFIIAMTGHETDYEW 304

Query: 1132 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 1191
            +    +     N ++  N   +K+ Q  L ++ +   L ++D++DINR+M  GE K R+A
Sbjct: 305  LVQYLRSTGIDNQVIAENEQEVKKAQSVLADIASTYGLSVSDIKDINRRMSIGEAKVRRA 364

Query: 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251
            K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 365  KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 424

Query: 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 1311
            RQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A +MEMPE+K+R
Sbjct: 425  RQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAERMEMPEDKVR 484

Query: 1312 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
            K++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P ++A  A +R   + +L  LT RE
Sbjct: 485  KVLKIAKEPISMETPIGDDEDSHLGDFIEDAKVLSPIESATIAGLRESTQSVLAGLTARE 544

Query: 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEGK 1430
            +KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ FL+G+
Sbjct: 545  AKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRCFLDGE 603



 Score =  549 bits (1415), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 294/584 (50%), Positives = 391/584 (66%), Gaps = 12/584 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  GK +GYLT++E+ND LP DI D E IE II     M I V E   D ++L+     
Sbjct: 13  LIAKGKAQGYLTYAEVNDHLPSDIADPEQIEDIIGMINDMGIQVYEDAPDEDSLITDGAA 72

Query: 106 -SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            + D+ ++   AAL++VDS+FGRT DP++MYMREMGSVELL R+ E++IAKRIEEG + +
Sbjct: 73  VTGDEDDDDEVAALASVDSEFGRTTDPVRMYMREMGSVELLNREDELKIAKRIEEGQQQV 132

Query: 165 IHAISSCPTTIMEILIAADKISKNE--IKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKI 222
           + AIS     + E +   D IS  E  I++ ++V G +D   S    V      N++   
Sbjct: 133 VRAISRSCKVVDEFIRDFDSISDEEGGIRLTDLVSGFVD--LSEPETVFSSQAANDD--- 187

Query: 223 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDK-MRKAFEKEGYNSESYIKAHNNISNE 281
              S   D   ++++ L Y  + +   +     K    A +K GY      +  + ++  
Sbjct: 188 ---SVDEDADEDEVKGLDYNDVKEKVEVLRKLHKSAAAAIKKHGYGDPKVNEKLDELAES 244

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
            +  ++  +  ++L  T+   +  + + E+ I ++ VN+  M R  FI     +E +  W
Sbjct: 245 FIEFKWAPQYFKRLTATVSEAVALIREKERLIADLCVNEAKMTRKEFIIAMTGHETDYEW 304

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
           +    +     N ++  N   +K+ Q  L ++ +   L ++D++DINR+M  GE K R+A
Sbjct: 305 LVQYLRSTGIDNQVIAENEQEVKKAQSVLADIASTYGLSVSDIKDINRRMSIGEAKVRRA 364

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 365 KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 424

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQAITRSIADQARTIRIPVHMIETINK++RISRQILQE G E  P  +A +MEMPE+K+R
Sbjct: 425 RQAITRSIADQARTIRIPVHMIETINKLNRISRQILQELGREATPEELAERMEMPEDKVR 484

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           K++KIAKEP+SME+P+GDDEDSHLGDFIED  +L+P ++A  A +R   + +L  LT RE
Sbjct: 485 KVLKIAKEPISMETPIGDDEDSHLGDFIEDAKVLSPIESATIAGLRESTQSVLAGLTARE 544

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 AKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 588


>gi|163751572|ref|ZP_02158794.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
 gi|161328580|gb|EDP99733.1| RNA polymerase sigma-70 factor [Shewanella benthica KT99]
          Length = 609

 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 309/602 (51%), Positives = 414/602 (68%), Gaps = 6/602 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  IL   D+    E+++ +I+ G ID N            ++  + 
Sbjct: 128  NTVQASVAEYPQAIAAILDQFDRYEAEEVRLSDIISGFIDPNADDIAPTATHVGSDLSQS 187

Query: 1012 ILIESSSADLSTEQLEKLK----YESLIKFSNI-SFHFDKMRKAFEKEGYNSESYIKAHN 1066
             L + +S D   E+ E  K     ES  +F+ +   H + +R   +K   + E+ + A  
Sbjct: 188  ELDKDNSKDDEDEEEEGPKGPDPEESKERFTQLREVHENTLRIIADKGRGHPEATV-ALF 246

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+K +  +E
Sbjct: 247  EIGELFKEFRLMPKQFDRLVKGMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKCYTADE 306

Query: 1127 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 1186
             ++ W D E   +  Y   L      ++  + KL  ++ +  L +  ++DINR+M  GE 
Sbjct: 307  SSIAWFDAELASKKPYVAGLQMVETDVRRCRFKLDIIEKETGLAIASIKDINRRMSIGEA 366

Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 367  KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 426

Query: 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306
            ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MP
Sbjct: 427  ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMP 486

Query: 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 1366
            E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   ++L  
Sbjct: 487  EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAG 546

Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK F
Sbjct: 547  LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSF 606

Query: 1427 LE 1428
            L+
Sbjct: 607  LD 608



 Score =  554 bits (1427), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 301/589 (51%), Positives = 405/589 (68%), Gaps = 6/589 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  IL   D+    E+++ +I+ G ID N            ++  + 
Sbjct: 128 NTVQASVAEYPQAIAAILDQFDRYEAEEVRLSDIISGFIDPNADDIAPTATHVGSDLSQS 187

Query: 222 ILIESSSADLSTEQLEKLK----YESLIKFSNI-SFHFDKMRKAFEKEGYNSESYIKAHN 276
            L + +S D   E+ E  K     ES  +F+ +   H + +R   +K   + E+ + A  
Sbjct: 188 ELDKDNSKDDEDEEEEGPKGPDPEESKERFTQLREVHENTLRIIADKGRGHPEATV-ALF 246

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+K +  +E
Sbjct: 247 EIGELFKEFRLMPKQFDRLVKGMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKCYTADE 306

Query: 337 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 396
            ++ W D E   +  Y   L      ++  + KL  ++ +  L +  ++DINR+M  GE 
Sbjct: 307 SSIAWFDAELASKKPYVAGLQMVETDVRRCRFKLDIIEKETGLAIASIKDINRRMSIGEA 366

Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
           KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 367 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 426

Query: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 516
           ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MP
Sbjct: 427 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMP 486

Query: 517 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 576
           E+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   ++L  
Sbjct: 487 EDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHEVLAG 546

Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 LTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 595


>gi|148979373|ref|ZP_01815479.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
 gi|145961809|gb|EDK27102.1| RNA polymerase sigma factor RpoD [Vibrionales bacterium SWAT-3]
          Length = 614

 Score =  569 bits (1466), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 310/611 (50%), Positives = 420/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123  KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  ++   A+   +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183  IGSELAETDLDDEDAEDVDDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S   + A   + +     R T K  + L + LRN +++V   E+ I+   V    MP+  
Sbjct: 243  SPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W+D        Y   + R+   I+   QKL  ++ +  L +  ++DI
Sbjct: 303  FIALFTGNESSEAWLDEVLASDKPYAEKIKRHENDIRRSIQKLDMIEKETSLTVQSIKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSETLRSFLD 613



 Score =  554 bits (1427), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 303/598 (50%), Positives = 411/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123 KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  ++   A+   +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183 IGSELAETDLDDEDAEDVDDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S   + A   + +     R T K  + L + LRN +++V   E+ I+   V    MP+  
Sbjct: 243 SPKAMLATTMMQDVFKEFRLTPKQFDYLVNELRNSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W+D        Y   + R+   I+   QKL  ++ +  L +  ++DI
Sbjct: 303 FIALFTGNESSEAWLDEVLASDKPYAEKIKRHENDIRRSIQKLDMIEKETSLTVQSIKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|331006388|ref|ZP_08329697.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
 gi|330419812|gb|EGG94169.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC1989]
          Length = 601

 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 303/615 (49%), Positives = 411/615 (66%), Gaps = 22/615 (3%)

Query: 820  SNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 879
            SN+++E      + K+LI  GKE+GYLT++++ND LP+DI D + +E II+    M I V
Sbjct: 2    SNNKQE-----SRIKLLIARGKEQGYLTYADVNDHLPQDISDPDQVEDIIQMINDMGIRV 56

Query: 880  SEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTR 937
             E+  D E L++++  S  D   + EAA +    +   GRT DP++MYMREMG+VELLTR
Sbjct: 57   YENAPDAEELLMTDGDSSADEIASAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTR 116

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 997
            +GEI IAKRIEEG +D++HA++  P  +  ++   D + K E +I +++ G +D      
Sbjct: 117  EGEIAIAKRIEEGTRDLMHALACWPNVVQILIDEFDLLVKEERRIPDLIAGWLDPADDVP 176

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                   KN  ++    +     L   ++ +       +F  +     K  K  +K G  
Sbjct: 177  AAGPAAQKNKTDDDEDEDEVDTGLDPVEVNE-------RFGALKKQLAKTDKIIKKHGRE 229

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+      + + + +   +   +  + +    R  +  V + E++IL + V    MPR  
Sbjct: 230  SKEAEAELSELGDIIKFFKLPPRQFDPMYKKARGVLESVRREERRILSLCVRTAKMPRKT 289

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVLPLND 1173
            FIK FP NE +  W+    + + DY+     N   +KE     Q+KL  +Q  + + L+ 
Sbjct: 290  FIKEFPGNETDPTWIPGVIEKKRDYSA----NFEEVKEEILRAQRKLDQIQNTVGIELSM 345

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            +++INR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 346  IKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 405

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 406  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 465

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  +MEMPEEK+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A +
Sbjct: 466  PTPEELGERMEMPEEKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTITSPVESATD 525

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              +    +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 526  VGLTESTRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 585

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 586  LRHPSRSDHLRSFLD 600



 Score =  554 bits (1427), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 296/602 (49%), Positives = 402/602 (66%), Gaps = 22/602 (3%)

Query: 30  SNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV 89
           SN+++E      + K+LI  GKE+GYLT++++ND LP+DI D + +E II+    M I V
Sbjct: 2   SNNKQE-----SRIKLLIARGKEQGYLTYADVNDHLPQDISDPDQVEDIIQMINDMGIRV 56

Query: 90  SEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTR 147
            E+  D E L++++  S  D   + EAA +    +   GRT DP++MYMREMG+VELLTR
Sbjct: 57  YENAPDAEELLMTDGDSSADEIASAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTR 116

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN 207
           +GEI IAKRIEEG +D++HA++  P  +  ++   D + K E +I +++ G +D      
Sbjct: 117 EGEIAIAKRIEEGTRDLMHALACWPNVVQILIDEFDLLVKEERRIPDLIAGWLDPADDVP 176

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                  KN  ++    +     L   ++ +       +F  +     K  K  +K G  
Sbjct: 177 AAGPAAQKNKTDDDEDEDEVDTGLDPVEVNE-------RFGALKKQLAKTDKIIKKHGRE 229

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S+      + + + +   +   +  + +    R  +  V + E++IL + V    MPR  
Sbjct: 230 SKEAEAELSELGDIIKFFKLPPRQFDPMYKKARGVLESVRREERRILSLCVRTAKMPRKT 289

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVLPLND 383
           FIK FP NE +  W+    + + DY+     N   +KE     Q+KL  +Q  + + L+ 
Sbjct: 290 FIKEFPGNETDPTWIPGVIEKKRDYSA----NFEEVKEEILRAQRKLDQIQNTVGIELSM 345

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           +++INR+M  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 346 IKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 405

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 406 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 465

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  +MEMPEEK+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P ++A +
Sbjct: 466 PTPEELGERMEMPEEKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDGTITSPVESATD 525

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             +    +D+L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 526 VGLTESTRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 585

Query: 624 LR 625
           LR
Sbjct: 586 LR 587


>gi|86148095|ref|ZP_01066395.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218708434|ref|YP_002416055.1| RNA polymerase sigma factor RpoD [Vibrio splendidus LGP32]
 gi|85834082|gb|EAQ52240.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|218321453|emb|CAV17405.1| RNA polymerase sigma factor rpoD (Sigma-70) [Vibrio splendidus LGP32]
          Length = 614

 Score =  568 bits (1465), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 311/611 (50%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123  KRIEDGINTVQLSVAEYPGTIPYILEQFDRVLAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   K  +E    + + +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183  IGSELAKTDLEDEDKEEAEDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S     A   + +     R T K  + L + LR  +++V   E+ I+   V    MP+  
Sbjct: 243  SPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W+D        Y   + RN   I+   QKL  ++ +  L +  ++DI
Sbjct: 303  FIALFTGNESSEAWLDEVLASDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSETLRSFLD 613



 Score =  553 bits (1426), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 304/598 (50%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123 KRIEDGINTVQLSVAEYPGTIPYILEQFDRVLAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   K  +E    + + +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183 IGSELAKTDLEDEDKEEAEDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S     A   + +     R T K  + L + LR  +++V   E+ I+   V    MP+  
Sbjct: 243 SPKATLATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W+D        Y   + RN   I+   QKL  ++ +  L +  ++DI
Sbjct: 303 FIALFTGNESSEAWLDEVLASDKPYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|387772261|ref|ZP_10128215.1| RNA polymerase sigma factor RpoD [Haemophilus parahaemolyticus HK385]
 gi|386907410|gb|EIJ72123.1| RNA polymerase sigma factor RpoD [Haemophilus parahaemolyticus HK385]
          Length = 623

 Score =  568 bits (1464), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 307/623 (49%), Positives = 406/623 (65%), Gaps = 36/623 (5%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12   QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIKVLETAPDTDEL 71

Query: 890  MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
            ML+ NIT +D VEEAT+  LSTV+S+ GRT DP+ MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72   MLAENITDEDVVEEATKV-LSTVESELGRTTDPVLMYMREMGTVELLTREDEIQISKRIE 130

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG----- 1003
            EG+ ++  A++  P  +  +L   D++    +++ +++   +D N    + V        
Sbjct: 131  EGINEVQCAVAEYPEALEGVLACYDEVEAGNMRLVDLITAFVDPNAQEEDPVDDDSIHLD 190

Query: 1004 ------------------NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 1045
                                NNN +     S   +L+ E           KF+ +    +
Sbjct: 191  DDAHPDVDDVEDEEEEDDGDNNNADSGDDNSIDPELARE-----------KFTALKEQHE 239

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            K   A  K G       +  N +S+     R   K  + L +T++  + QV   E+QI  
Sbjct: 240  KALLAIRKHGRTHAKAREQINALSDIFREFRLVPKQFDLLVETMQKLMKQVRAEERQIQR 299

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V   GM +  F+K F  NE +  W++     +      L   +  I+     L NL+ 
Sbjct: 300  YAVEYAGMKKADFLKNFQGNETSEAWMEKAINAKRGGVPKLANYVEKIRVNIVNLQNLEQ 359

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
            +  L ++ +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 360  NSGLTISQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 419

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 420  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 479

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 480  CLQEMGREATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 539

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 540  LPLDSATAESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 599

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 600  IEAKALRKLRHPSRSETLRSFLD 622



 Score =  553 bits (1425), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 300/610 (49%), Positives = 397/610 (65%), Gaps = 36/610 (5%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + ++LI  G+E+GYL  SE++D LPE+++D E IE II+    M I V E   DT+ L
Sbjct: 12  QSQIELLIAQGREQGYLILSEVHDHLPEELVDAEQIEDIIQMITDMGIKVLETAPDTDEL 71

Query: 100 MLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           ML+ NIT +D VEEAT+  LSTV+S+ GRT DP+ MYMREMG+VELLTR+ EI+I+KRIE
Sbjct: 72  MLAENITDEDVVEEATKV-LSTVESELGRTTDPVLMYMREMGTVELLTREDEIQISKRIE 130

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG----- 213
           EG+ ++  A++  P  +  +L   D++    +++ +++   +D N    + V        
Sbjct: 131 EGINEVQCAVAEYPEALEGVLACYDEVEAGNMRLVDLITAFVDPNAQEEDPVDDDSIHLD 190

Query: 214 ------------------NKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFD 255
                               NNN +     S   +L+ E           KF+ +    +
Sbjct: 191 DDAHPDVDDVEDEEEEDDGDNNNADSGDDNSIDPELARE-----------KFTALKEQHE 239

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           K   A  K G       +  N +S+     R   K  + L +T++  + QV   E+QI  
Sbjct: 240 KALLAIRKHGRTHAKAREQINALSDIFREFRLVPKQFDLLVETMQKLMKQVRAEERQIQR 299

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V   GM +  F+K F  NE +  W++     +      L   +  I+     L NL+ 
Sbjct: 300 YAVEYAGMKKADFLKNFQGNETSEAWMEKAINAKRGGVPKLANYVEKIRVNIVNLQNLEQ 359

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
           +  L ++ +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 360 NSGLTISQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 419

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 420 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 479

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 480 CLQEMGREATPEELAERMNMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 539

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 540 LPLDSATAESLRIATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 599

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 600 IEAKALRKLR 609


>gi|410623859|ref|ZP_11334669.1| RNA polymerase primary sigma factor [Glaciecola pallidula DSM 14239 =
            ACAM 615]
 gi|410156555|dbj|GAC30043.1| RNA polymerase primary sigma factor [Glaciecola pallidula DSM 14239 =
            ACAM 615]
          Length = 608

 Score =  568 bits (1463), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 306/607 (50%), Positives = 418/607 (68%), Gaps = 4/607 (0%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GK++GYLTF+E+ND LP++I+D + IE II+    M I VSE   D
Sbjct: 1    MQSKQSQIKLLIAKGKDQGYLTFAEVNDHLPQNIVDSDQIEDIIRMINDMGIKVSESAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             + L++   T+D+DV EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61   ADELLMQESTADEDVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 1002
            RIE+G+  +  +++  P  I  +L   D     EI+I +I+ G +D N    +     I 
Sbjct: 121  RIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRISDIIIGFVDPNEQDVAPTATHIG 180

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
               +  E     + S  +   E+   +  E +  KF+ +   + K+      +G + ++ 
Sbjct: 181  SELSQKELDDEDDDSDDEEEEEEDTGVDPELAREKFTALRKQYTKVMSVIAVKGRSHKAS 240

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             K  + +S      R   K  +++   +R  +++V   E+ I++  V    MP+  FIK 
Sbjct: 241  RKEIHELSEVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKYCVMNAKMPKKDFIKA 300

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE + +W+    + +  Y   L      I+    K+  ++ +  L + D++DINR+M
Sbjct: 301  FAGNETSTDWLYKALEGKAPYVEKLLEFKEEIERSVSKMNAVEAETGLIIPDIKDINRRM 360

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 361  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 420

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ 
Sbjct: 421  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSE 480

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+++  +
Sbjct: 481  RMLMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKNATQ 540

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 541  EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 600

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 601  QLRSFLD 607



 Score =  552 bits (1423), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 299/594 (50%), Positives = 408/594 (68%), Gaps = 4/594 (0%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GK++GYLTF+E+ND LP++I+D + IE II+    M I VSE   D
Sbjct: 1   MQSKQSQIKLLIAKGKDQGYLTFAEVNDHLPQNIVDSDQIEDIIRMINDMGIKVSESAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            + L++   T+D+DV EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEIEIAK
Sbjct: 61  ADELLMQESTADEDVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIEIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIK 212
           RIE+G+  +  +++  P  I  +L   D     EI+I +I+ G +D N    +     I 
Sbjct: 121 RIEDGINQVQCSVAEYPEAITYLLDQWDLYEAEEIRISDIIIGFVDPNEQDVAPTATHIG 180

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKEGYNSESY 271
              +  E     + S  +   E+   +  E +  KF+ +   + K+      +G + ++ 
Sbjct: 181 SELSQKELDDEDDDSDDEEEEEEDTGVDPELAREKFTALRKQYTKVMSVIAVKGRSHKAS 240

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            K  + +S      R   K  +++   +R  +++V   E+ I++  V    MP+  FIK 
Sbjct: 241 RKEIHELSEVFKEFRLIPKQFDRMVKNMRGMMDRVRIQERLIMKYCVMNAKMPKKDFIKA 300

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE + +W+    + +  Y   L      I+    K+  ++ +  L + D++DINR+M
Sbjct: 301 FAGNETSTDWLYKALEGKAPYVEKLLEFKEEIERSVSKMNAVEAETGLIIPDIKDINRRM 360

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 361 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 420

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  ++ 
Sbjct: 421 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSE 480

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  ++ P D+A   S+++  +
Sbjct: 481 RMLMPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIIQPLDSATGGSLKNATQ 540

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 541 EVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|430377017|ref|ZP_19431150.1| RNA polymerase sigma factor 70 [Moraxella macacae 0408225]
 gi|429540154|gb|ELA08183.1| RNA polymerase sigma factor 70 [Moraxella macacae 0408225]
          Length = 633

 Score =  568 bits (1463), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/633 (48%), Positives = 424/633 (66%), Gaps = 37/633 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+   +   LI++GKE+GYLT++EIND LP+ +I+ + IE II+    + I + E   D 
Sbjct: 5    EHSTSQLATLIQMGKEQGYLTYAEINDQLPDSVIESDQIEDIIQMLSDVGIKIFEIAPDE 64

Query: 887  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            + +MLS N   D+   +   A L++V+S+ GRT DP++MYMREMG+V+LLTR+GEI IAK
Sbjct: 65   DDIMLSDNSNDDEIAADEAAAVLASVESEPGRTTDPVRMYMREMGTVDLLTREGEIAIAK 124

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE+G++D+ +A++  P T+  +L    +  + E K+ +IV G +D   SS++  I    
Sbjct: 125  RIEDGVRDVQYAMTFWPGTVELVLSEYQETFEGEKKVSDIVTGFLDA--SSDDVEIGEGS 182

Query: 1006 NNNEEKIL----------------IESSSADLSTEQ--------------LEKLKYESLI 1035
            +  +  IL                 E +   L T++              LE++K     
Sbjct: 183  DKIDLPILPKKTLADKDLDDLDSETEETDDSLETDEIGDDGETDDTIGLDLEEVKN---- 238

Query: 1036 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 1095
            +F  +   +   + A EK G  SE   +A+ +++N  +  + T +  + + D +R     
Sbjct: 239  RFIELEKLYQVAKTATEKHGRASEQSTQAYQDLANYFMLFKLTGRIADIIMDMMRAVYED 298

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V + E+ I+++V+ +  MP+  F K FP NE NL+W+ N    + D+   L + +  +  
Sbjct: 299  VRKHERHIMKLVIRRGKMPKDEFRKTFPNNETNLDWLPNRIAGKPDFADNLSKILDEVLL 358

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
             Q K+ + +T + + +N ++ + R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 359  HQGKIADYETKLGMDINQMKKVARNMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGL 418

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 419  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 478

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INKI+R+SRQ+LQE G EP P  +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHL
Sbjct: 479  INKINRVSRQLLQEMGREPTPEELGCRLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHL 538

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED ++ +P D A    ++   +++L +LT RE+KVL+MRFGI+M++DHTLEEVGKQ
Sbjct: 539  GDFIEDSSINSPVDEATAQGLKEATREVLANLTDREAKVLKMRFGIDMATDHTLEEVGKQ 598

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            FDVTRERIRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 599  FDVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 631



 Score =  551 bits (1420), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 296/620 (47%), Positives = 415/620 (66%), Gaps = 37/620 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+   +   LI++GKE+GYLT++EIND LP+ +I+ + IE II+    + I + E   D 
Sbjct: 5   EHSTSQLATLIQMGKEQGYLTYAEINDQLPDSVIESDQIEDIIQMLSDVGIKIFEIAPDE 64

Query: 97  ETLMLS-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           + +MLS N   D+   +   A L++V+S+ GRT DP++MYMREMG+V+LLTR+GEI IAK
Sbjct: 65  DDIMLSDNSNDDEIAADEAAAVLASVESEPGRTTDPVRMYMREMGTVDLLTREGEIAIAK 124

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE+G++D+ +A++  P T+  +L    +  + E K+ +IV G +D   SS++  I    
Sbjct: 125 RIEDGVRDVQYAMTFWPGTVELVLSEYQETFEGEKKVSDIVTGFLDA--SSDDVEIGEGS 182

Query: 216 NNNEEKIL----------------IESSSADLSTEQ--------------LEKLKYESLI 245
           +  +  IL                 E +   L T++              LE++K     
Sbjct: 183 DKIDLPILPKKTLADKDLDDLDSETEETDDSLETDEIGDDGETDDTIGLDLEEVKN---- 238

Query: 246 KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ 305
           +F  +   +   + A EK G  SE   +A+ +++N  +  + T +  + + D +R     
Sbjct: 239 RFIELEKLYQVAKTATEKHGRASEQSTQAYQDLANYFMLFKLTGRIADIIMDMMRAVYED 298

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V + E+ I+++V+ +  MP+  F K FP NE NL+W+ N    + D+   L + +  +  
Sbjct: 299 VRKHERHIMKLVIRRGKMPKDEFRKTFPNNETNLDWLPNRIAGKPDFADNLSKILDEVLL 358

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
            Q K+ + +T + + +N ++ + R M  GE KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 359 HQGKIADYETKLGMDINQMKKVARNMSVGEAKARRAKKEMVEANLRLVISIAKKYTNRGL 418

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 419 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 478

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INKI+R+SRQ+LQE G EP P  +  +++M E K+RK++KIAKEP+SME+P+GDDEDSHL
Sbjct: 479 INKINRVSRQLLQEMGREPTPEELGCRLDMDEAKVRKVLKIAKEPISMETPIGDDEDSHL 538

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDFIED ++ +P D A    ++   +++L +LT RE+KVL+MRFGI+M++DHTLEEVGKQ
Sbjct: 539 GDFIEDSSINSPVDEATAQGLKEATREVLANLTDREAKVLKMRFGIDMATDHTLEEVGKQ 598

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 599 FDVTRERIRQIEAKALRKLR 618


>gi|334705854|ref|ZP_08521720.1| RNA polymerase sigma factor RpoD [Aeromonas caviae Ae398]
          Length = 618

 Score =  568 bits (1463), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/617 (49%), Positives = 420/617 (68%), Gaps = 27/617 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8    QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68   AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 995
            +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128  INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNEVDDVAPTATHIGSELS 187

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
             ++   +    + +E    ++S  D       ++  E   KF  +   ++  R + ++ G
Sbjct: 188  EDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQQNG 244

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
               +    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245  RAHDDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPL 1171
              F+  F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +
Sbjct: 305  KTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSI 360

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361  AQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP+P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA
Sbjct: 481  REPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAA 540

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
             + S+R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541  TSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 601  RKLRHPSRSEVLRSFLD 617



 Score =  553 bits (1426), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/604 (49%), Positives = 411/604 (68%), Gaps = 27/604 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP+DI+D + IE II+    M I V E+  D + L++
Sbjct: 8   QLKLLVAKGKEQGYLTYAEVNDHLPQDIVDSDQIEDIIQMINDMGIQVVENAPDADDLIM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           +   T+D+D  EA   AL++V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G
Sbjct: 68  AEGGTADEDAAEAAAQALASVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------------FS 205
           +  +  +++  P  I  +L   DK    ++++ +I+ G ID N                S
Sbjct: 128 INQVQSSVAEYPEAITYLLEQYDKYEAEQLRLSDIISGFIDPNEVDDVAPTATHIGSELS 187

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
            ++   +    + +E    ++S  D       ++  E   KF  +   ++  R + ++ G
Sbjct: 188 EDDLADEDEDEDEDEDEDGDNSDDDGDGGPDPEVARE---KFGELRAQYEVTRLSIQQNG 244

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
              +    A   +++     R   K  ++L + +R  + +V   E+ I+++ V +  MP+
Sbjct: 245 RAHDDTQNAIAQLADVFRQFRLMPKQFDRLVNNMREMMERVRVQERIIMKLCVEQAKMPK 304

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRN----IPSIKELQQKLINLQTDIVLPL 381
             F+  F  NE    W + + +    ++  L       + SI +LQQ    ++ +  L +
Sbjct: 305 KTFVAAFTNNECETAWFEYQKQAGKAWSPRLLEMDEEVLRSIGKLQQ----IEEETGLSI 360

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 361 AQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 420

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 421 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 480

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP+P  +A++M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P+DAA
Sbjct: 481 REPNPEELAMRMGMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLALPADAA 540

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
            + S+R+  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 541 TSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 622 RKLR 625
           RKLR
Sbjct: 601 RKLR 604


>gi|407069934|ref|ZP_11100772.1| RNA polymerase sigma factor RpoD [Vibrio cyclitrophicus ZF14]
          Length = 614

 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 310/611 (50%), Positives = 418/611 (68%), Gaps = 9/611 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123  KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 1057
              +   +  +E    + + +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183  IGSELAETDLEDEDKEEAEDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S     A   + +     R T K  + L + LR  +++V   E+ I+   V    MP+  
Sbjct: 243  SPKATIATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI +F  NE +  W+D        Y   + RN   I+   QKL  ++ +  L +  ++DI
Sbjct: 303  FIALFTGNESSEAWLDEVLASDKPYAEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDI 362

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363  SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483  ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 543  GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 602

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 603  SRSETLRSFLD 613



 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 303/598 (50%), Positives = 409/598 (68%), Gaps = 9/598 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKLLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L L++  ++  +D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDANIDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  +++  P TI  IL   D++   EI++ ++++G +D +          +
Sbjct: 123 KRIEDGINTVQLSVAEYPGTIPYILEQFDRVQAEEIRLTDLINGFVDPDDDGTAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYN 267
             +   +  +E    + + +  E+ + ++ I       KF+ +   +   + A  + G+ 
Sbjct: 183 IGSELAETDLEDEDKEEAEDDEEEEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHE 242

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S     A   + +     R T K  + L + LR  +++V   E+ I+   V    MP+  
Sbjct: 243 SPKATIATTMMQDVFKEFRLTPKQFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKS 302

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI +F  NE +  W+D        Y   + RN   I+   QKL  ++ +  L +  ++DI
Sbjct: 303 FIALFTGNESSEAWLDEVLASDKPYAEKIKRNEHDIRRSIQKLDMIERETSLTVQSIKDI 362

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 363 SRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 422

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P 
Sbjct: 423 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPE 482

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R
Sbjct: 483 ELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLR 542

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 543 GATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|90407543|ref|ZP_01215725.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
 gi|90311353|gb|EAS39456.1| RNA polymerase sigma factor RpoD [Psychromonas sp. CNPT3]
          Length = 610

 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 315/616 (51%), Positives = 408/616 (66%), Gaps = 33/616 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+G+LT++E+ND LP+DI + E IE II+    M I V E   D + + L
Sbjct: 8    QLKELIIKGKEKGFLTYAEVNDHLPQDIFEAEQIEDIIQMIGDMGIKVYETAPDADEISL 67

Query: 892  ---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
               SN T+D+D  EA    L+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIE
Sbjct: 68   GEESNDTADEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNNR 999
            EG+K++  ++S  P TI  +L   D     E+K+ +++ G ID N          +  + 
Sbjct: 128  EGIKEVQTSVSEYPGTITGLLDNWDSYEAEEMKLTDMISGFIDPNDDMTQAPTATNVGSE 187

Query: 1000 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
            +    K +NEE+   E        E       ES  KF+ +      +     K G    
Sbjct: 188  LTDAQKKDNEEEDEEEEGPKGPCPE-------ESAEKFTELRRLNTIVEDMIAKHGRAHA 240

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
                A N  +      +   K  +++  T+R  +N V   E+ +L+I V +  MP+  FI
Sbjct: 241  KTRTAINAQAEFFQQFKLIPKQFDRMVKTIRASMNMVRTQERLVLKICVEQNKMPKKAFI 300

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN-------LQTDIVLPLN 1172
             +F  NE N  W+D     + +Y          IKE  + L+        ++T   L + 
Sbjct: 301  SLFKGNETNKAWLDAIYATEKEY-------AKRIKEFDEDLVRCIRKMALVETQTALTII 353

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +L++I+RKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354  NLKEISRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 414  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 473

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            +P P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D A 
Sbjct: 474  DPHPDELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIALPVDCAT 533

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            + S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534  SESLKNATNEVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR  +L+ FL+
Sbjct: 594  KLRHPSRSEQLRSFLD 609



 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 308/603 (51%), Positives = 398/603 (66%), Gaps = 33/603 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+G+LT++E+ND LP+DI + E IE II+    M I V E   D + + L
Sbjct: 8   QLKELIIKGKEKGFLTYAEVNDHLPQDIFEAEQIEDIIQMIGDMGIKVYETAPDADEISL 67

Query: 102 ---SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
              SN T+D+D  EA    L+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIE
Sbjct: 68  GEESNDTADEDAVEAAAQVLATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAKRIE 127

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---------FSSNNR 209
           EG+K++  ++S  P TI  +L   D     E+K+ +++ G ID N          +  + 
Sbjct: 128 EGIKEVQTSVSEYPGTITGLLDNWDSYEAEEMKLTDMISGFIDPNDDMTQAPTATNVGSE 187

Query: 210 VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSE 269
           +    K +NEE+   E        E       ES  KF+ +      +     K G    
Sbjct: 188 LTDAQKKDNEEEDEEEEGPKGPCPE-------ESAEKFTELRRLNTIVEDMIAKHGRAHA 240

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
               A N  +      +   K  +++  T+R  +N V   E+ +L+I V +  MP+  FI
Sbjct: 241 KTRTAINAQAEFFQQFKLIPKQFDRMVKTIRASMNMVRTQERLVLKICVEQNKMPKKAFI 300

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN-------LQTDIVLPLN 382
            +F  NE N  W+D     + +Y          IKE  + L+        ++T   L + 
Sbjct: 301 SLFKGNETNKAWLDAIYATEKEY-------AKRIKEFDEDLVRCIRKMALVETQTALTII 353

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +L++I+RKM  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354 NLKEISRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 414 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 473

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           +P P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D A 
Sbjct: 474 DPHPDELAERMMMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIALPVDCAT 533

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           + S+++   ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534 SESLKNATNEVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 623 KLR 625
           KLR
Sbjct: 594 KLR 596


>gi|167622943|ref|YP_001673237.1| RNA polymerase sigma 70 subunit RpoD [Shewanella halifaxensis
            HAW-EB4]
 gi|167352965|gb|ABZ75578.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella halifaxensis
            HAW-EB4]
          Length = 615

 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 309/605 (51%), Positives = 417/605 (68%), Gaps = 9/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKGNKNNN 1008
              +  +++  P  I  IL   D+    E+++ +I+ G +D N    +     +  + +++
Sbjct: 131  NTVQASVAEYPQAIAMILEQFDRYEAEEVRLSDIISGFVDPNAEDVAPTATHVGSDLSDD 190

Query: 1009 EEKILIESSSADLSTEQLEKLKY----ESLIKFSNISF-HFDKMRKAFEKEGYNSESYIK 1063
            +     +    D   E+ E  K     E+  KF+ +   H + +R   +K   + ES + 
Sbjct: 191  DLDDEDDDDDDDDDDEEEEGPKGPDPEEAKEKFTTLRVAHENALRIIADKGRGHPESTV- 249

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       R   K  ++L   +R+ +++V   E+ I+++ V +  MP+ +F+KV+ 
Sbjct: 250  ALFEIGEIFKEFRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYT 309

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE ++ W + E      Y   L      ++  + KL  ++T+  L +  ++DINR+M  
Sbjct: 310  SNESSIEWFNEELASGKPYAEGLKVVSFDVQRCRAKLDAIETETGLAIGAIKDINRRMSI 369

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 430  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 489

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++
Sbjct: 490  LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEV 549

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 550  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 609

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 610  KSFLD 614



 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 301/592 (50%), Positives = 408/592 (68%), Gaps = 9/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKGNKNNN 218
             +  +++  P  I  IL   D+    E+++ +I+ G +D N    +     +  + +++
Sbjct: 131 NTVQASVAEYPQAIAMILEQFDRYEAEEVRLSDIISGFVDPNAEDVAPTATHVGSDLSDD 190

Query: 219 EEKILIESSSADLSTEQLEKLKY----ESLIKFSNISF-HFDKMRKAFEKEGYNSESYIK 273
           +     +    D   E+ E  K     E+  KF+ +   H + +R   +K   + ES + 
Sbjct: 191 DLDDEDDDDDDDDDDEEEEGPKGPDPEEAKEKFTTLRVAHENALRIIADKGRGHPESTV- 249

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       R   K  ++L   +R+ +++V   E+ I+++ V +  MP+ +F+KV+ 
Sbjct: 250 ALFEIGEIFKEFRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYT 309

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE ++ W + E      Y   L      ++  + KL  ++T+  L +  ++DINR+M  
Sbjct: 310 SNESSIEWFNEELASGKPYAEGLKVVSFDVQRCRAKLDAIETETGLAIGAIKDINRRMSI 369

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 370 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 429

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 430 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 489

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++
Sbjct: 490 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEV 549

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|294139649|ref|YP_003555627.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
 gi|7388082|sp|O24744.1|RPOD_SHEVD RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|1912047|dbj|BAA19475.1| RNA polymerase sigma factor [Shewanella violacea]
 gi|293326118|dbj|BAJ00849.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
          Length = 614

 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/606 (50%), Positives = 410/606 (67%), Gaps = 9/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   TEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+    E+++ +I+ G ID N +  +      G+  +  
Sbjct: 128  YTVQASVAEYPPAIASILDQFDRYEAEEVRLSDIISGFIDPNAADIAPTATHIGSDLSQS 187

Query: 1010 EKILIESSSADLSTEQLEKL-------KYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
            E+   +S       ++ E+          ES  +F+ +    +   K    +G       
Sbjct: 188  ERDKDDSKDDSKDDDEDEEEEGPKGPDPEESKERFTQLREVHENTLKIIADKGRGHPEAT 247

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+K +
Sbjct: 248  VALFEIGELFKEFRLMPKQFDRLVKNMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKGY 307

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              +E ++ W D E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M 
Sbjct: 308  TADESSIAWFDTELASKKPYAEGLKMIEPDVRRCRFKLDIIEKETGLAIASIKDINRRMS 367

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 487

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   +
Sbjct: 488  MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHE 547

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 548  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEI 607

Query: 1423 LKIFLE 1428
            LK FL+
Sbjct: 608  LKSFLD 613



 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/593 (50%), Positives = 401/593 (67%), Gaps = 9/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  TEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+    E+++ +I+ G ID N +  +      G+  +  
Sbjct: 128 YTVQASVAEYPPAIASILDQFDRYEAEEVRLSDIISGFIDPNAADIAPTATHIGSDLSQS 187

Query: 220 EKILIESSSADLSTEQLEKL-------KYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
           E+   +S       ++ E+          ES  +F+ +    +   K    +G       
Sbjct: 188 ERDKDDSKDDSKDDDEDEEEEGPKGPDPEESKERFTQLREVHENTLKIIADKGRGHPEAT 247

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+K +
Sbjct: 248 VALFEIGELFKEFRLMPKQFDRLVKNMRATMDKVRVQERLIMKLCVEQAKMPKKNFVKGY 307

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             +E ++ W D E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M 
Sbjct: 308 TADESSIAWFDTELASKKPYAEGLKMIEPDVRRCRFKLDIIEKETGLAIASIKDINRRMS 367

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAER 487

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+R+   +
Sbjct: 488 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLRNATHE 547

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|410617504|ref|ZP_11328471.1| RNA polymerase primary sigma factor [Glaciecola polaris LMG 21857]
 gi|410162958|dbj|GAC32609.1| RNA polymerase primary sigma factor [Glaciecola polaris LMG 21857]
          Length = 612

 Score =  567 bits (1462), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 309/624 (49%), Positives = 421/624 (67%), Gaps = 34/624 (5%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1    MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            ++ L++     D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61   SDELLMQENAPDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121  RIEEGINQVQCSVAEYPEAITYLLDQWDMFEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 1006 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEG-- 1055
             +   +  ++    D      E  +         E+  KFS +   ++K R     +G  
Sbjct: 181  GSELSEEDLDDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKARDVIASKGRS 240

Query: 1056 -YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
              NS   I A + I  E    R   K  +++   +R+ ++++   E+ +++  V    MP
Sbjct: 241  HANSRKEIDALSEIFKEF---RLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVVTAKMP 297

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQ 1164
            +  FIK F  NE + +W+            IL  ++P  +E++           K+  ++
Sbjct: 298  KKDFIKAFSGNETSTDWLFE----------ILASSVPYAEEIRVHQEELERSIGKMNAVE 347

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 348  DETGLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 407

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 408  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 467

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 468  QMLQEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTI 527

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
            + P D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 528  VQPLDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 587

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR  +L+ FL+
Sbjct: 588  QIEAKALRKLRHPSRSEQLRSFLD 611



 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 411/611 (67%), Gaps = 34/611 (5%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           +++ + + K+LI  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E+  D
Sbjct: 1   MQSKQSQIKLLIAKGKEQGYLTFAEVNDHLPQDIVDSDQIEDIIRMINDMGIKVFENAPD 60

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           ++ L++     D++V EA   AL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAK
Sbjct: 61  SDELLMQENAPDEEVAEAAAQALATVESEIGRTTDPVRMYMREMGTVELLTREGEIVIAK 120

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIEEG+  +  +++  P  I  +L   D     EI++ +I+ G +D N + N      + 
Sbjct: 121 RIEEGINQVQCSVAEYPEAITYLLDQWDMFEAEEIRLSDIIVGFVDPNEADNIAPTATHI 180

Query: 216 NNNEEKILIESSSADLSTEQLEKLKY--------ESLIKFSNISFHFDKMRKAFEKEG-- 265
            +   +  ++    D      E  +         E+  KFS +   ++K R     +G  
Sbjct: 181 GSELSEEDLDDEDDDGDDSDDEDEEEEDTGPDPEEAREKFSELRVQYEKARDVIASKGRS 240

Query: 266 -YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
             NS   I A + I  E    R   K  +++   +R+ ++++   E+ +++  V    MP
Sbjct: 241 HANSRKEIDALSEIFKEF---RLVPKQFDRMVKNMRSMMDRIRVQERIVMKHCVVTAKMP 297

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQ 374
           +  FIK F  NE + +W+            IL  ++P  +E++           K+  ++
Sbjct: 298 KKDFIKAFSGNETSTDWLFE----------ILASSVPYAEEIRVHQEELERSIGKMNAVE 347

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 348 DETGLIIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 407

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 408 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 467

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  ++ +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 468 QMLQEMGREPTPEELSERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTI 527

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
           + P D+A   S+++  +++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 528 VQPLDSATGGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 587

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 588 QIEAKALRKLR 598


>gi|127511929|ref|YP_001093126.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637224|gb|ABO22867.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella loihica PV-4]
          Length = 616

 Score =  567 bits (1461), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/605 (50%), Positives = 412/605 (68%), Gaps = 8/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++D+D  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDSTDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 1007
              +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   +     ++
Sbjct: 131  NTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDIISGFVDPNAEDMAPTATHIGSELSDD 190

Query: 1008 NEEKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            + +    E    D   ++ +  K     E+  +F+ +    +K  K  E +G        
Sbjct: 191  DLDDEDDEGDDEDDDGDEEDSPKGPDPEEARERFTQLREAHEKALKVIELKGREHPEATA 250

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A  +I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+KV+ 
Sbjct: 251  ALFDIGEIFKEFRLVPKQFDRLVKNMREMMDKVRIQERLIMKLCVEQAKMPKKNFVKVYT 310

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE ++ W + E   +  Y   L      ++  + KL  ++ +  L +  ++DINR+M  
Sbjct: 311  SNESSIEWFNEEIAAKKPYAEGLEMVAEDVQRCRAKLDAIENETGLAIAAIKDINRRMSI 370

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 431  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 490

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++
Sbjct: 491  LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEV 550

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 551  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEIL 610

Query: 1424 KIFLE 1428
            K FL+
Sbjct: 611  KSFLD 615



 Score =  552 bits (1423), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 296/592 (50%), Positives = 403/592 (68%), Gaps = 8/592 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++D+D  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDSTDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 217
             +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   +     ++
Sbjct: 131 NTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDIISGFVDPNAEDMAPTATHIGSELSDD 190

Query: 218 NEEKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIK 273
           + +    E    D   ++ +  K     E+  +F+ +    +K  K  E +G        
Sbjct: 191 DLDDEDDEGDDEDDDGDEEDSPKGPDPEEARERFTQLREAHEKALKVIELKGREHPEATA 250

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A  +I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+KV+ 
Sbjct: 251 ALFDIGEIFKEFRLVPKQFDRLVKNMREMMDKVRIQERLIMKLCVEQAKMPKKNFVKVYT 310

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE ++ W + E   +  Y   L      ++  + KL  ++ +  L +  ++DINR+M  
Sbjct: 311 SNESSIEWFNEEIAAKKPYAEGLEMVAEDVQRCRAKLDAIENETGLAIAAIKDINRRMSI 370

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 371 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 430

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 431 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 490

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++
Sbjct: 491 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEV 550

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|343512082|ref|ZP_08749227.1| RNA polymerase sigma factor RpoD [Vibrio scophthalmi LMG 19158]
 gi|343515428|ref|ZP_08752485.1| RNA polymerase sigma factor RpoD [Vibrio sp. N418]
 gi|342796433|gb|EGU32116.1| RNA polymerase sigma factor RpoD [Vibrio scophthalmi LMG 19158]
 gi|342798466|gb|EGU34079.1| RNA polymerase sigma factor RpoD [Vibrio sp. N418]
          Length = 618

 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 313/622 (50%), Positives = 412/622 (66%), Gaps = 27/622 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE------------------SLIKFSNISFHFDK 1046
                   I  E +  DL  E  +                       +L KF+ +   F  
Sbjct: 183  -------IGSELTETDLKDEDDDSDDDSDDSDEEEAEEDTGIDPELALEKFTALRNTFQN 235

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
             + A  + G++S     AH  + +     R T K  + L + LR  + +V   E+ I++ 
Sbjct: 236  HQLAVNEHGHDSAQAQDAHALVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKA 295

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
             V    MP+  FI +F  NE +  W+D        Y   + ++   I+    KL  ++ +
Sbjct: 296  TVEYGKMPKKSFITLFTGNESSDAWLDEVLASDKPYADKIRQSEDDIRRSILKLKIIEEE 355

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 356  TSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 415

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 416  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 475

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 476  LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 535

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P D+A   S+R+  KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 536  PLDSATATSLRAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 595

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKLRHPSR   L+ FL+
Sbjct: 596  EAKALRKLRHPSRSETLRSFLD 617



 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 306/609 (50%), Positives = 403/609 (66%), Gaps = 27/609 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE------------------SLIKFSNISFHFDK 256
                  I  E +  DL  E  +                       +L KF+ +   F  
Sbjct: 183 -------IGSELTETDLKDEDDDSDDDSDDSDEEEAEEDTGIDPELALEKFTALRNTFQN 235

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
            + A  + G++S     AH  + +     R T K  + L + LR  + +V   E+ I++ 
Sbjct: 236 HQLAVNEHGHDSAQAQDAHALVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKA 295

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
            V    MP+  FI +F  NE +  W+D        Y   + ++   I+    KL  ++ +
Sbjct: 296 TVEYGKMPKKSFITLFTGNESSDAWLDEVLASDKPYADKIRQSEDDIRRSILKLKIIEEE 355

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 356 TSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 415

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+
Sbjct: 416 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM 475

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  
Sbjct: 476 LQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLEL 535

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P D+A   S+R+  KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQI
Sbjct: 536 PLDSATATSLRAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 595

Query: 617 EAKALRKLR 625
           EAKALRKLR
Sbjct: 596 EAKALRKLR 604


>gi|148653373|ref|YP_001280466.1| RNA polymerase sigma-70 subunit RpoD [Psychrobacter sp. PRwf-1]
 gi|148572457|gb|ABQ94516.1| RNA polymerase, sigma 70 subunit, RpoD [Psychrobacter sp. PRwf-1]
          Length = 623

 Score =  567 bits (1460), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/615 (47%), Positives = 419/615 (68%), Gaps = 23/615 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +   LI++GKE+GYLT++E+ND LP  I + + IE I++    + I + E   D + +++
Sbjct: 12   QLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 892  SNITSDDDVE-EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            ++  +DDD+  +   A L+ V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72   NDGANDDDMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            ++D+ HA++  P T+  IL   D +   E K+ +++ G +D        V       +EE
Sbjct: 132  IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVITGFLDPEEIEPAVV-----EEDEE 186

Query: 1011 KILI---ESSSADLSTEQLEKLKYESLI--------------KFSNISFHFDKMRKAFEK 1053
            KI +   +S + D+  E  E+   E                 +   I   F   ++A E+
Sbjct: 187  KIPVITTKSKAKDVDDEDDEEEAEEEEEAEESGGLDPELVRQRVEEIRELFAVAKQALEQ 246

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G  S    +A+  ++   + ++   +  + +   + +  + V + E+QI+ +V+ +  M
Sbjct: 247  YGRGSAQAEEAYAQLAERFMLLKLNNRMADNVMAIMHDVYDDVRKQERQIMRLVIRRGKM 306

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            PR  F K FP NE N++W+ +  K    +   L + +  +  LQ+++ + +  + + + +
Sbjct: 307  PRSEFRKTFPSNETNVDWLTDRLKGNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMQITE 366

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++++ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 367  MKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 426

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 427  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 486

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P + A +
Sbjct: 487  PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATS 546

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
            A ++   +D+L++LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 547  AGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 606

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FLE
Sbjct: 607  LRHPSRSEHLRSFLE 621



 Score =  550 bits (1417), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 287/602 (47%), Positives = 410/602 (68%), Gaps = 23/602 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +   LI++GKE+GYLT++E+ND LP  I + + IE I++    + I + E   D + +++
Sbjct: 12  QLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 102 SNITSDDDVE-EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           ++  +DDD+  +   A L+ V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72  NDGANDDDMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           ++D+ HA++  P T+  IL   D +   E K+ +++ G +D        V       +EE
Sbjct: 132 IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVITGFLDPEEIEPAVV-----EEDEE 186

Query: 221 KILI---ESSSADLSTEQLEKLKYESLI--------------KFSNISFHFDKMRKAFEK 263
           KI +   +S + D+  E  E+   E                 +   I   F   ++A E+
Sbjct: 187 KIPVITTKSKAKDVDDEDDEEEAEEEEEAEESGGLDPELVRQRVEEIRELFAVAKQALEQ 246

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G  S    +A+  ++   + ++   +  + +   + +  + V + E+QI+ +V+ +  M
Sbjct: 247 YGRGSAQAEEAYAQLAERFMLLKLNNRMADNVMAIMHDVYDDVRKQERQIMRLVIRRGKM 306

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           PR  F K FP NE N++W+ +  K    +   L + +  +  LQ+++ + +  + + + +
Sbjct: 307 PRSEFRKTFPSNETNVDWLTDRLKGNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMQITE 366

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++++ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 367 MKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 426

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 427 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 486

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P + A +
Sbjct: 487 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDATS 546

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
           A ++   +D+L++LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 547 AGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 606

Query: 624 LR 625
           LR
Sbjct: 607 LR 608


>gi|170725515|ref|YP_001759541.1| RNA polymerase sigma 70 subunit RpoD [Shewanella woodyi ATCC 51908]
 gi|169810862|gb|ACA85446.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella woodyi ATCC 51908]
          Length = 611

 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 303/603 (50%), Positives = 413/603 (68%), Gaps = 6/603 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8    QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEMMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNE 1009
              +  +++  P  I  IL   D+    EI++ +I+ G +D N    +      G++ ++E
Sbjct: 128  NTVQASVAEYPQAIAMILEQYDRYEAEEIRLSDIISGFVDPNAEDVAPTATHVGSELSDE 187

Query: 1010 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
            +    +   ++   ++ E  K     E+  +F+ +    +   +    +G        A 
Sbjct: 188  DLDDEDDEDSEDDEDEEEGPKGPDPEEAKERFTQLREAHENTLRVINLKGRGHPESTLAL 247

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              I       R   K  ++L  ++R  +++V   E+ I+++ V +  MP+ +F+K +  +
Sbjct: 248  FEIGEIFKEFRLMPKQFDRLVKSMRAMMDRVRVQERLIMKLCVEQAKMPKKNFVKGYTSD 307

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E ++ W D E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M  GE
Sbjct: 308  ESSIAWFDEELASKKPYVEGLEMVEPDVRRCRAKLDAIEKETGLAIAAIKDINRRMSIGE 367

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 368  AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M M
Sbjct: 428  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLM 487

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++L 
Sbjct: 488  PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLA 547

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK 
Sbjct: 548  GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKS 607

Query: 1426 FLE 1428
            FL+
Sbjct: 608  FLD 610



 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 295/590 (50%), Positives = 404/590 (68%), Gaps = 6/590 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 8   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEMMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS--SNNRVIKGNKNNNE 219
             +  +++  P  I  IL   D+    EI++ +I+ G +D N    +      G++ ++E
Sbjct: 128 NTVQASVAEYPQAIAMILEQYDRYEAEEIRLSDIISGFVDPNAEDVAPTATHVGSELSDE 187

Query: 220 EKILIESSSADLSTEQLEKLK----YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
           +    +   ++   ++ E  K     E+  +F+ +    +   +    +G        A 
Sbjct: 188 DLDDEDDEDSEDDEDEEEGPKGPDPEEAKERFTQLREAHENTLRVINLKGRGHPESTLAL 247

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             I       R   K  ++L  ++R  +++V   E+ I+++ V +  MP+ +F+K +  +
Sbjct: 248 FEIGEIFKEFRLMPKQFDRLVKSMRAMMDRVRVQERLIMKLCVEQAKMPKKNFVKGYTSD 307

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E ++ W D E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M  GE
Sbjct: 308 ESSIAWFDEELASKKPYVEGLEMVEPDVRRCRAKLDAIEKETGLAIAAIKDINRRMSIGE 367

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 368 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 427

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M M
Sbjct: 428 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLM 487

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++L 
Sbjct: 488 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLA 547

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|261492895|ref|ZP_05989441.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica serotype A2 str. BOVINE]
 gi|261496755|ref|ZP_05993130.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica serotype A2 str. OVINE]
 gi|261307594|gb|EEY08922.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica serotype A2 str. OVINE]
 gi|261311436|gb|EEY12593.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica serotype A2 str. BOVINE]
          Length = 623

 Score =  566 bits (1459), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/605 (50%), Positives = 405/605 (66%), Gaps = 14/605 (2%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ L+L+ NI 
Sbjct: 19   ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDTDDLLLAENIA 78

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 79   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 1013
             AI+  P  +  +L    ++   E+++ ++V   +D N      +  I+     +EE   
Sbjct: 138  CAIAEYPEALSGLLACYAQVETGEMRLSDLVTAFVDPNILEEAPLEDIEAALGEDEESSD 197

Query: 1014 IESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
            +     +   E  +     S            KF  +    +K+    +K G  S+   +
Sbjct: 198  VPDVDDENEDEDGDSSSDSSDDSSIDPELAREKFEALRSQHEKVLLVIQKHGRTSKKSKE 257

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +S+     R  +K  + L  +++  + QV   E+QI    V   GM +  F+K F 
Sbjct: 258  QIEILSHIFREFRLVSKQFDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQ 317

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             +E++  W++     + +    L   + +I+     L NL+    L +  +R+I  ++  
Sbjct: 318  GHELSEAWIEKAINAKKNAVPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISN 377

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 378  GELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 437

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A +M
Sbjct: 438  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERM 497

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    ++
Sbjct: 498  GMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEV 557

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 558  LEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETL 617

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 618  RSFLD 622



 Score =  551 bits (1420), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 297/592 (50%), Positives = 396/592 (66%), Gaps = 14/592 (2%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ L+L+ NI 
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDTDDLLLAENIA 78

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 79  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 223
            AI+  P  +  +L    ++   E+++ ++V   +D N      +  I+     +EE   
Sbjct: 138 CAIAEYPEALSGLLACYAQVETGEMRLSDLVTAFVDPNILEEAPLEDIEAALGEDEESSD 197

Query: 224 IESSSADLSTEQLEKLKYESLI----------KFSNISFHFDKMRKAFEKEGYNSESYIK 273
           +     +   E  +     S            KF  +    +K+    +K G  S+   +
Sbjct: 198 VPDVDDENEDEDGDSSSDSSDDSSIDPELAREKFEALRSQHEKVLLVIQKHGRTSKKSKE 257

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +S+     R  +K  + L  +++  + QV   E+QI    V   GM +  F+K F 
Sbjct: 258 QIEILSHIFREFRLVSKQFDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQ 317

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            +E++  W++     + +    L   + +I+     L NL+    L +  +R+I  ++  
Sbjct: 318 GHELSEAWIEKAINAKKNAVPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISN 377

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 378 GELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 437

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A +M
Sbjct: 438 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERM 497

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    ++
Sbjct: 498 GMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEV 557

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 558 LEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|165976903|ref|YP_001652496.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 3 str. JL03]
 gi|303252483|ref|ZP_07338647.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 2 str. 4226]
 gi|307248518|ref|ZP_07530536.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 2 str. S1536]
 gi|307250749|ref|ZP_07532682.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 4 str. M62]
 gi|307261955|ref|ZP_07543613.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 12 str. 1096]
 gi|165877004|gb|ABY70052.1| RNA polymerase sigma factor [Actinobacillus pleuropneumoniae serovar
            3 str. JL03]
 gi|302648684|gb|EFL78876.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 2 str. 4226]
 gi|306854994|gb|EFM87179.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 2 str. S1536]
 gi|306857217|gb|EFM89340.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 4 str. M62]
 gi|306868366|gb|EFN00185.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 12 str. 1096]
          Length = 619

 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 306/623 (49%), Positives = 408/623 (65%), Gaps = 50/623 (8%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 1002
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1003 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
                          GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194  VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 1049 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239  QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296  YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQ 355

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356  TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476  CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536  LPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 596  IEAKALRKLRHPSRSETLRSFLD 618



 Score =  551 bits (1419), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/610 (49%), Positives = 399/610 (65%), Gaps = 50/610 (8%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 212
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 213 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
                         GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194 VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 259 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239 QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296 YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQ 355

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356 TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476 CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536 LPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 596 IEAKALRKLR 605


>gi|157960786|ref|YP_001500820.1| RNA polymerase sigma-70 subunit RpoD [Shewanella pealeana ATCC
            700345]
 gi|157845786|gb|ABV86285.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella pealeana ATCC
            700345]
          Length = 616

 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 309/606 (50%), Positives = 415/606 (68%), Gaps = 10/606 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 1007
              +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   V     ++
Sbjct: 131  NTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDIISGFVDPNAEDVAPTATHVGSELSDD 190

Query: 1008 NEEKILIESSSADLSTEQLEKLKY----ESLIKFSNISF-HFDKMRKAFEKEGYNSESYI 1062
              +    +    D   E+ E  K     E+  KF+ +   H + +R   +K   + ES +
Sbjct: 191  ELDDEDDDDDDDDDDDEEEEGPKGPDPEEAKEKFTTLRLAHENALRIIADKGRGHPESTV 250

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
             A   I       R   K  ++L   +R+ +++V   E+ I+++ V +  MP+ +F+KV+
Sbjct: 251  -ALFEIGEIFKEFRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVY 309

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              NE ++ W ++E      Y   L      ++  + KL  ++ +  L +  ++DINR+M 
Sbjct: 310  TSNESSIEWFNDELASGKPYVEGLQMVEFDVQRCRAKLDAIEVETGLAIGAIKDINRRMS 369

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370  IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 430  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 489

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   +
Sbjct: 490  MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHE 549

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   
Sbjct: 550  VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEI 609

Query: 1423 LKIFLE 1428
            LK FL+
Sbjct: 610  LKSFLD 615



 Score =  551 bits (1420), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 301/593 (50%), Positives = 406/593 (68%), Gaps = 10/593 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEQAPDADEIMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++DDD  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDSTDDDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 217
             +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   V     ++
Sbjct: 131 NTVQASVAEYPQAIAMILEQYDRYEAEEVRLSDIISGFVDPNAEDVAPTATHVGSELSDD 190

Query: 218 NEEKILIESSSADLSTEQLEKLKY----ESLIKFSNISF-HFDKMRKAFEKEGYNSESYI 272
             +    +    D   E+ E  K     E+  KF+ +   H + +R   +K   + ES +
Sbjct: 191 ELDDEDDDDDDDDDDDEEEEGPKGPDPEEAKEKFTTLRLAHENALRIIADKGRGHPESTV 250

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
            A   I       R   K  ++L   +R+ +++V   E+ I+++ V +  MP+ +F+KV+
Sbjct: 251 -ALFEIGEIFKEFRLMPKQFDRLVKNMRSMMDKVRVQERLIMKLCVEQAKMPKKNFVKVY 309

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             NE ++ W ++E      Y   L      ++  + KL  ++ +  L +  ++DINR+M 
Sbjct: 310 TSNESSIEWFNDELASGKPYVEGLQMVEFDVQRCRAKLDAIEVETGLAIGAIKDINRRMS 369

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAER 489

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   +
Sbjct: 490 MLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHE 549

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|303250977|ref|ZP_07337166.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 6 str. Femo]
 gi|307253124|ref|ZP_07535005.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 6 str. Femo]
 gi|302650194|gb|EFL80361.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 6 str. Femo]
 gi|306859418|gb|EFM91450.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 6 str. Femo]
          Length = 619

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 306/623 (49%), Positives = 408/623 (65%), Gaps = 50/623 (8%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 1002
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1003 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
                          GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194  VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 1049 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239  QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296  YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLTNYIDQIRVNIDNLQRMEQ 355

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356  TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476  CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536  LPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 596  IEAKALRKLRHPSRSETLRSFLD 618



 Score =  551 bits (1419), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/610 (49%), Positives = 399/610 (65%), Gaps = 50/610 (8%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 212
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 213 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
                         GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194 VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 259 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239 QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296 YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLTNYIDQIRVNIDNLQRMEQ 355

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356 TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476 CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536 LPLDSATAESLRLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 596 IEAKALRKLR 605


>gi|392546486|ref|ZP_10293623.1| RNA polymerase sigma factor [Pseudoalteromonas rubra ATCC 29570]
          Length = 614

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 314/607 (51%), Positives = 407/607 (67%), Gaps = 9/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V+E   D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVAESAPDVDELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEILIAKRIEEGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  +L   DK    E+++ +IV G  D +   +   I      +E  
Sbjct: 128  NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVTGFFD-SLEDDEAPISATHIGSELS 186

Query: 1012 ILIESSSADLSTEQLEKLKYESLIKFSNISF-HFDKMR-------KAFEKEGYNSESYIK 1063
                    D   E  +  +         I+  HF+++R       K FE +G        
Sbjct: 187  EEDLDDEDDDGDEDDDDSEDADTGPDPEIAREHFEELRTLYNNARKCFEVKGRAHPDSQA 246

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
            A   I       +   K  +++ + +R+ +++V   E+ I++       +P+  FIK F 
Sbjct: 247  AIAEIGELFRKFKLVPKQFDRMVNNMRDMMDRVRVQERIIMKQACQIAKLPKKTFIKHFA 306

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             NE ++ WVD E      ++  L +  P I+    KL  ++    L +  ++DINR+M  
Sbjct: 307  NNETDMAWVDAEIAAGDKHSAKLAQVKPEIERCVNKLTAIEESTGLSIERIKDINRRMSI 366

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367  GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 427  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 486

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    ++
Sbjct: 487  MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPVDSATMESLRGATNEV 546

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 547  LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 606

Query: 1424 KIFLEGK 1430
            K FL+ K
Sbjct: 607  KSFLDVK 613



 Score =  550 bits (1418), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 308/600 (51%), Positives = 400/600 (66%), Gaps = 10/600 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID + +E II     M I V+E   D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSDQVEDIISMINDMGIQVAESAPDVDELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEILIAKRIEEGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  +L   DK    E+++ +IV G  D +   +   I      +E  
Sbjct: 128 NQVQISVAEYPEAITYLLEQWDKYEAEEMRLSDIVTGFFD-SLEDDEAPISATHIGSELS 186

Query: 222 ILIESSSADLSTEQLEKLKYESLIKFSNISF-HFDKMR-------KAFEKEGYNSESYIK 273
                   D   E  +  +         I+  HF+++R       K FE +G        
Sbjct: 187 EEDLDDEDDDGDEDDDDSEDADTGPDPEIAREHFEELRTLYNNARKCFEVKGRAHPDSQA 246

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
           A   I       +   K  +++ + +R+ +++V   E+ I++       +P+  FIK F 
Sbjct: 247 AIAEIGELFRKFKLVPKQFDRMVNNMRDMMDRVRVQERIIMKQACQIAKLPKKTFIKHFA 306

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            NE ++ WVD E      ++  L +  P I+    KL  ++    L +  ++DINR+M  
Sbjct: 307 NNETDMAWVDAEIAAGDKHSAKLAQVKPEIERCVNKLTAIEESTGLSIERIKDINRRMSI 366

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 367 GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 426

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M
Sbjct: 427 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERM 486

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+R    ++
Sbjct: 487 MMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIESPVDSATMESLRGATNEV 546

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D L
Sbjct: 547 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDLL 606


>gi|343506739|ref|ZP_08744209.1| RNA polymerase sigma factor RpoD [Vibrio ichthyoenteri ATCC 700023]
 gi|342801842|gb|EGU37298.1| RNA polymerase sigma factor RpoD [Vibrio ichthyoenteri ATCC 700023]
          Length = 619

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 313/623 (50%), Positives = 412/623 (66%), Gaps = 28/623 (4%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFD 1045
                   I  E +  DL  E  +  +                     +L KF+ +   F 
Sbjct: 183  -------IGSELTETDLKDEDDDSEEDSDDDSDDEEAEEDTGIDPELALEKFTALRNTFQ 235

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
              + A  + G  S    +AH  + +     R T K  + L + LR  + +V   E+ I++
Sbjct: 236  NHQLAVNEHGQESAQAQQAHELVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMK 295

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V    MP+  FI +F  NE +  W+D        Y   + ++   I+    KL  ++ 
Sbjct: 296  ATVEYGKMPKKSFITLFTGNESSNAWLDEVLASDKPYADKIRQSEDDIRRSILKLKIIEE 355

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
            +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356  ETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 476  MLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE 535

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+R+  KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536  LPLDSATATSLRAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 596  IEAKALRKLRHPSRSETLRSFLD 618



 Score =  551 bits (1419), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 306/610 (50%), Positives = 403/610 (66%), Gaps = 28/610 (4%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDAITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFD 255
                  I  E +  DL  E  +  +                     +L KF+ +   F 
Sbjct: 183 -------IGSELTETDLKDEDDDSEEDSDDDSDDEEAEEDTGIDPELALEKFTALRNTFQ 235

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
             + A  + G  S    +AH  + +     R T K  + L + LR  + +V   E+ I++
Sbjct: 236 NHQLAVNEHGQESAQAQQAHELVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMK 295

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V    MP+  FI +F  NE +  W+D        Y   + ++   I+    KL  ++ 
Sbjct: 296 ATVEYGKMPKKSFITLFTGNESSNAWLDEVLASDKPYADKIRQSEDDIRRSILKLKIIEE 355

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
           +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356 ETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 476 MLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLE 535

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+R+  KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536 LPLDSATATSLRAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 596 IEAKALRKLR 605


>gi|326794299|ref|YP_004312119.1| RNA polymerase sigma-70 subunit RpoD [Marinomonas mediterranea MMB-1]
 gi|326545063|gb|ADZ90283.1| RNA polymerase, sigma 70 subunit, RpoD [Marinomonas mediterranea
            MMB-1]
          Length = 610

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 305/616 (49%), Positives = 403/616 (65%), Gaps = 33/616 (5%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLTF+E+ND LP+D+ D E +E I+     M I VSE+  D E+L++
Sbjct: 8    RLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIVAMINDMGIVVSEYAPDKESLLM 67

Query: 892  S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
                ++D++  E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68   EEGDSTDEEAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++++ ++S  P  +  +L    +  + E ++ +I  G ID               + EE
Sbjct: 128  TREVMASLSYFPGAVDVLLDTYARTVEEEGRLSDIFSGFID--------------GDGEE 173

Query: 1011 KILIESSSADLSTEQLEKLKY------------------ESLIKFSNISFHFDKMRKAFE 1052
             I  E     +  E+ E  +                   E+  +F+ I     ++    E
Sbjct: 174  PIFEEVIEEVVEEEEDESDEEESSDDDEEEETESGPDPEETARRFNEIKRIHHEVLALLE 233

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
                   +       +S     I+   K  + L D +R+++++V + E+ I+++ V K G
Sbjct: 234  NSDRQDPAVRAKQEELSISFAPIKLVPKLFDDLIDRVRSRMDKVREQERLIMQVCVRKAG 293

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F+K FP NE N  W+  +  +   Y+  L  N       Q+KL  +  D  L + 
Sbjct: 294  MPRTEFLKRFPSNETNPGWLQEQIDLSASYSAALEENEAEFSRSQRKLRAISKDTGLSIA 353

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
             L++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354  QLKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 414  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 473

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            E  P  +A++M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A 
Sbjct: 474  EATPEELAVRMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPVDTAT 533

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
               ++     +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534  IEGLKESTTTVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FL+
Sbjct: 594  KLRHPSRSEHLRSFLD 609



 Score =  550 bits (1418), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 298/603 (49%), Positives = 394/603 (65%), Gaps = 33/603 (5%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLTF+E+ND LP+D+ D E +E I+     M I VSE+  D E+L++
Sbjct: 8   RLKELIAKGKEQGYLTFTEVNDHLPDDLSDPEQVEEIVAMINDMGIVVSEYAPDKESLLM 67

Query: 102 S-NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
               ++D++  E   AAL+ V+ D  RT DP++MYMREMG+VELLTR GEI IAKRIEEG
Sbjct: 68  EEGDSTDEEAAEEAAAALAAVEGDVARTTDPVRMYMREMGTVELLTRAGEIAIAKRIEEG 127

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++++ ++S  P  +  +L    +  + E ++ +I  G ID               + EE
Sbjct: 128 TREVMASLSYFPGAVDVLLDTYARTVEEEGRLSDIFSGFID--------------GDGEE 173

Query: 221 KILIESSSADLSTEQLEKLKY------------------ESLIKFSNISFHFDKMRKAFE 262
            I  E     +  E+ E  +                   E+  +F+ I     ++    E
Sbjct: 174 PIFEEVIEEVVEEEEDESDEEESSDDDEEEETESGPDPEETARRFNEIKRIHHEVLALLE 233

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
                  +       +S     I+   K  + L D +R+++++V + E+ I+++ V K G
Sbjct: 234 NSDRQDPAVRAKQEELSISFAPIKLVPKLFDDLIDRVRSRMDKVREQERLIMQVCVRKAG 293

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F+K FP NE N  W+  +  +   Y+  L  N       Q+KL  +  D  L + 
Sbjct: 294 MPRTEFLKRFPSNETNPGWLQEQIDLSASYSAALEENEAEFSRSQRKLRAISKDTGLSIA 353

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
            L++INR++  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 354 QLKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 413

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G 
Sbjct: 414 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 473

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           E  P  +A++M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED+   +P D A 
Sbjct: 474 EATPEELAVRMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDDGAESPVDTAT 533

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
              ++     +L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 534 IEGLKESTTTVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 623 KLR 625
           KLR
Sbjct: 594 KLR 596


>gi|374618894|ref|ZP_09691428.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium HIMB55]
 gi|374302121|gb|EHQ56305.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium HIMB55]
          Length = 601

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 299/596 (50%), Positives = 412/596 (69%), Gaps = 14/596 (2%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS--NI 894
            I  GKE+GYLT++E+ND LP+DI + + +E II+    M I V E   D + L+L+  + 
Sbjct: 15   IAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELILTEGDR 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++++
Sbjct: 75   SADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGIREL 134

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNEEKI 1012
            + A++  P     +    D ++K E K+ +I+ G +D   +  S   + + N N+  +  
Sbjct: 135  MAALAYYPRVARRLCEEYDLVAKEERKLSDILVGYLDPADHVPSAQEIAEQNANSGND-- 192

Query: 1013 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 1072
              +S   D   + +E  K     +F+ +     K     E++GY+S+   K    +    
Sbjct: 193  --DSEETDTGPDPVEAKK-----RFTALKRQCTKTENVLEEKGYDSKEAQKEMAKLGELF 245

Query: 1073 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 1132
               + T +  + L +T R  +  V + E++I+ +VV +C M R  FIK F  +E  L+W+
Sbjct: 246  KFFKLTPRVFDPLVETPRAVLAVVRESEREIMRLVVRECRMDRKEFIKSFQGSESKLDWI 305

Query: 1133 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 1192
            D  TK + D N  L      I  LQ+++  ++ ++ L   ++++INR+M  GE +AR+AK
Sbjct: 306  DGATK-KADVNERLANYREDIVRLQKRIAIIEDEVGLSTTEIKEINRRMSMGEARARRAK 364

Query: 1193 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252
            +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 365  KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 424

Query: 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 1312
            QAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+MPE+K+RK
Sbjct: 425  QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKVRK 484

Query: 1313 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 1372
            ++KIAKEP+SME+P+GDDEDS LGDFIED  + +P ++A    +    +++L  LT RE+
Sbjct: 485  VLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVESATEEGLTEATREVLGGLTAREA 544

Query: 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ FL+
Sbjct: 545  KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSFLD 600



 Score =  555 bits (1430), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 296/591 (50%), Positives = 407/591 (68%), Gaps = 15/591 (2%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS--NI 104
           I  GKE+GYLT++E+ND LP+DI + + +E II+    M I V E   D + L+L+  + 
Sbjct: 15  IAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELILTEGDR 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++++
Sbjct: 75  SADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGIREL 134

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK--NFSSNNRVIKGNKNNNEEKI 222
           + A++  P     +    D ++K E K+ +I+ G +D   +  S   + + N N+  +  
Sbjct: 135 MAALAYYPRVARRLCEEYDLVAKEERKLSDILVGYLDPADHVPSAQEIAEQNANSGND-- 192

Query: 223 LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEM 282
             +S   D   + +E  K     +F+ +     K     E++GY+S+   K    +    
Sbjct: 193 --DSEETDTGPDPVEAKK-----RFTALKRQCTKTENVLEEKGYDSKEAQKEMAKLGELF 245

Query: 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 342
              + T +  + L +T R  +  V + E++I+ +VV +C M R  FIK F  +E  L+W+
Sbjct: 246 KFFKLTPRVFDPLVETPRAVLAVVRESEREIMRLVVRECRMDRKEFIKSFQGSESKLDWI 305

Query: 343 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           D  TK + D N  L      I  LQ+++  ++ ++ L   ++++INR+M  GE +AR+AK
Sbjct: 306 DGATK-KADVNERLANYREDIVRLQKRIAIIEDEVGLSTTEIKEINRRMSMGEARARRAK 364

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 365 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 424

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +M+MPE+K+RK
Sbjct: 425 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMDMPEDKVRK 484

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           ++KIAKEP+SME+P+GDDEDS LGDFIED  + +P ++A    +    +++L  LT RE+
Sbjct: 485 VLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVESATEEGLTEATREVLGGLTAREA 544

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D+L
Sbjct: 545 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYL 595


>gi|254362696|ref|ZP_04978782.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica PHL213]
 gi|452745676|ref|ZP_21945509.1| RNA polymerase sigma factor RpoD [Mannheimia haemolytica serotype 6
            str. H23]
 gi|153094317|gb|EDN75178.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
            haemolytica PHL213]
 gi|452086278|gb|EME02668.1| RNA polymerase sigma factor RpoD [Mannheimia haemolytica serotype 6
            str. H23]
          Length = 623

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 304/605 (50%), Positives = 407/605 (67%), Gaps = 14/605 (2%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   D + L+L+ NI 
Sbjct: 19   ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDADDLLLAENIA 78

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 79   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEK-- 1011
             AI+  P  +  +L    ++   E+++ ++V   +D N      +  I+     +EE   
Sbjct: 138  CAIAEYPEALSGLLACYAQVETGEMRLSDLVTAFVDPNILEEAPLEDIEAALGEDEESSD 197

Query: 1012 -ILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSESYIK 1063
               ++  + D + +       +S I       KF  +    +K+    +K G  S+   +
Sbjct: 198  VPDVDDENEDENGDSSSDSSDDSSIDPELAREKFEALRSQHEKVLLVIQKHGRTSKKSKE 257

Query: 1064 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 1123
                +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F+K F 
Sbjct: 258  QIEILSHIFREFRLVPKQFDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQ 317

Query: 1124 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
             +E++  W++     + +    L   + +I+     L NL+    L +  +R+I  ++  
Sbjct: 318  GHELSEAWIEKAINAKKNAAPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISN 377

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 378  GELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 437

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A +M
Sbjct: 438  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERM 497

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    ++
Sbjct: 498  GMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEV 557

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L
Sbjct: 558  LEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETL 617

Query: 1424 KIFLE 1428
            + FL+
Sbjct: 618  RSFLD 622



 Score =  550 bits (1417), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 297/592 (50%), Positives = 398/592 (67%), Gaps = 14/592 (2%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   D + L+L+ NI 
Sbjct: 19  ISQGREQGYLTLSEVHDHLPEELVDAEQIEDIIQMINDMGIQVLEAAPDADDLLLAENIA 78

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 79  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 137

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEK-- 221
            AI+  P  +  +L    ++   E+++ ++V   +D N      +  I+     +EE   
Sbjct: 138 CAIAEYPEALSGLLACYAQVETGEMRLSDLVTAFVDPNILEEAPLEDIEAALGEDEESSD 197

Query: 222 -ILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSESYIK 273
              ++  + D + +       +S I       KF  +    +K+    +K G  S+   +
Sbjct: 198 VPDVDDENEDENGDSSSDSSDDSSIDPELAREKFEALRSQHEKVLLVIQKHGRTSKKSKE 257

Query: 274 AHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFP 333
               +S+     R   K  + L  +++  + QV   E+QI    V   GM +  F+K F 
Sbjct: 258 QIEILSHIFREFRLVPKQFDLLVASMQKLMKQVRTEERQIQRYAVEYAGMKKADFLKAFQ 317

Query: 334 ENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIA 393
            +E++  W++     + +    L   + +I+     L NL+    L +  +R+I  ++  
Sbjct: 318 GHELSEAWIEKAINAKKNAAPKLANYVDNIRVNIANLQNLEQTSGLTIAQIREIGGRISN 377

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 378 GELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 437

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A +M
Sbjct: 438 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAERM 497

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    ++
Sbjct: 498 GMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRMATNEV 557

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 558 LEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|413959714|ref|ZP_11398945.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. SJ98]
 gi|413939664|gb|EKS71632.1| RNA polymerase sigma-70 subunit RpoD [Burkholderia sp. SJ98]
          Length = 607

 Score =  565 bits (1456), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 273/615 (44%), Positives = 413/615 (67%), Gaps = 13/615 (2%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +KS+ ++  +      + LI++GK++G++T ++IND L  D+    ++E I + F  M +
Sbjct: 1    MKSDRQQGTDEHEWAIRALIRIGKDQGFVTHAQINDHLAGDLAQMTMVEDISRAFHEMGL 60

Query: 878  SVSEHVLDTETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVE 933
            +V EH   TETL+L    SN T DD   E  E ALS VDS+FGRT DP++MYMREMG+ +
Sbjct: 61   AVYEHAPSTETLLLDDAVSNDTLDDQSGEDDEFALSAVDSEFGRTTDPVRMYMREMGAKQ 120

Query: 934  LLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN 993
            LLTR  E+EIA+RIE+ L +MI AI+SCP TI  IL +A  +++ ++ IDE++DG+ D++
Sbjct: 121  LLTRKAEVEIARRIEDSLNEMIQAIASCPPTISMILASAQLVAEGKLGIDEMIDGIDDES 180

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 1053
              +   + +   +N +     E ++  L   +L +L  + L  F  +    D++R+A E 
Sbjct: 181  MPAAAEIDESAPHNGQSDSEAEDNADQL---RLTRLMTDGLALFGRVRECVDQLREAGET 237

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
               N++  I+       E+  +RFTA+ + + CD ++ ++ +V QIE++I  I +++C M
Sbjct: 238  HAPNAQETIR------KELGRVRFTARIVGQACDDMQQRLARVRQIEQRISSIAIDRCSM 291

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            PR  FI +FP +E +L+W         DY   L R++ +++  Q +L++++    +P+  
Sbjct: 292  PREQFIALFPGHETDLDWTTKTAAKSLDYGASLERSVAAVRAEQYQLMDIERHAAMPIQR 351

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            L+  +R ++A E + R+AK EM EANLRLVISIAKKY +RG  FLDLIQEGNIGLMKAVD
Sbjct: 352  LKQTSRHLLAAESRLRRAKDEMIEANLRLVISIAKKYVNRGAHFLDLIQEGNIGLMKAVD 411

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEY+RG+KFSTYA+WW+RQA+TR++ADQART+RIPVHM+E INK++RIS ++ Q TG  
Sbjct: 412  KFEYKRGWKFSTYASWWVRQAVTRAVADQARTVRIPVHMVEIINKLNRISNELRQHTGKP 471

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
              P+ +A +ME+PE +IR I KIA  P+S+++P  DD D+ LGD IED ++ +P +  + 
Sbjct: 472  ALPAALAERMELPEAQIRGIQKIAMHPISLQTPANDDADATLGDLIEDADVESPLEVVVR 531

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              MR  + D LN+L PRE++VLRMRFGI + ++ TL EV     V+RER+RQIE++A+RK
Sbjct: 532  TGMRVAIDDALNTLLPREARVLRMRFGINVPTEFTLGEVSSHLGVSRERVRQIESQAIRK 591

Query: 1414 LRHPSRYYKLKIFLE 1428
            L HPSR  KL+ F++
Sbjct: 592  LMHPSRADKLRSFID 606



 Score =  550 bits (1416), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 266/601 (44%), Positives = 403/601 (67%), Gaps = 13/601 (2%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           +KS+ ++  +      + LI++GK++G++T ++IND L  D+    ++E I + F  M +
Sbjct: 1   MKSDRQQGTDEHEWAIRALIRIGKDQGFVTHAQINDHLAGDLAQMTMVEDISRAFHEMGL 60

Query: 88  SVSEHVLDTETLML----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVE 143
           +V EH   TETL+L    SN T DD   E  E ALS VDS+FGRT DP++MYMREMG+ +
Sbjct: 61  AVYEHAPSTETLLLDDAVSNDTLDDQSGEDDEFALSAVDSEFGRTTDPVRMYMREMGAKQ 120

Query: 144 LLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN 203
           LLTR  E+EIA+RIE+ L +MI AI+SCP TI  IL +A  +++ ++ IDE++DG+ D++
Sbjct: 121 LLTRKAEVEIARRIEDSLNEMIQAIASCPPTISMILASAQLVAEGKLGIDEMIDGIDDES 180

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
             +   + +   +N +     E ++  L   +L +L  + L  F  +    D++R+A E 
Sbjct: 181 MPAAAEIDESAPHNGQSDSEAEDNADQL---RLTRLMTDGLALFGRVRECVDQLREAGET 237

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
              N++  I+       E+  +RFTA+ + + CD ++ ++ +V QIE++I  I +++C M
Sbjct: 238 HAPNAQETIR------KELGRVRFTARIVGQACDDMQQRLARVRQIEQRISSIAIDRCSM 291

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           PR  FI +FP +E +L+W         DY   L R++ +++  Q +L++++    +P+  
Sbjct: 292 PREQFIALFPGHETDLDWTTKTAAKSLDYGASLERSVAAVRAEQYQLMDIERHAAMPIQR 351

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           L+  +R ++A E + R+AK EM EANLRLVISIAKKY +RG  FLDLIQEGNIGLMKAVD
Sbjct: 352 LKQTSRHLLAAESRLRRAKDEMIEANLRLVISIAKKYVNRGAHFLDLIQEGNIGLMKAVD 411

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEY+RG+KFSTYA+WW+RQA+TR++ADQART+RIPVHM+E INK++RIS ++ Q TG  
Sbjct: 412 KFEYKRGWKFSTYASWWVRQAVTRAVADQARTVRIPVHMVEIINKLNRISNELRQHTGKP 471

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
             P+ +A +ME+PE +IR I KIA  P+S+++P  DD D+ LGD IED ++ +P +  + 
Sbjct: 472 ALPAALAERMELPEAQIRGIQKIAMHPISLQTPANDDADATLGDLIEDADVESPLEVVVR 531

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             MR  + D LN+L PRE++VLRMRFGI + ++ TL EV     V+RER+RQIE++A+RK
Sbjct: 532 TGMRVAIDDALNTLLPREARVLRMRFGINVPTEFTLGEVSSHLGVSRERVRQIESQAIRK 591

Query: 624 L 624
           L
Sbjct: 592 L 592


>gi|339477924|ref|YP_004706744.1| putative RNA polymerase sigma factor RpoD [Candidatus Moranella
            endobia PCIT]
 gi|338172475|gb|AEI74876.1| putative RNA polymerase sigma factor RpoD [Candidatus Moranella
            endobia PCIT]
          Length = 611

 Score =  565 bits (1455), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 313/623 (50%), Positives = 413/623 (66%), Gaps = 36/623 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K+L+  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D 
Sbjct: 3    QNQQSQLKLLVTHGKEQGYLTFAEVNDHLPDDIVDSDQIEDIIQMINDMGIRVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + L+L   T+ D  E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63   DDLLLLADTNPDTDEDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 122

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-------SS 996
            AKRIE+G+  +  +++     I  +L   D++   E ++ +++ G +D +         +
Sbjct: 123  AKRIEDGINQVQCSVAEYLKAISYLLEQYDRVEAGEARLSDLITGFVDSSVVEEMMLAPT 182

Query: 997  NNRV-IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 1055
            N R  +  N+  +EE+    S   D S +    L  +   KF  +   ++  RK  +  G
Sbjct: 183  NVRSELATNEITDEEEHDEASKEDDNSIDP--GLARQ---KFVELREQYEMTRKVIKTNG 237

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             N          +S      R   K  + L + +R  + +V   E+ I+++ V+   MP+
Sbjct: 238  RNHTKSAAELMKLSTVFKQFRLIPKLFDYLVNNMRAMMTRVRTQERVIMKLCVDISKMPK 297

Query: 1116 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQT 1165
             +FI +F  NE +  W          +   L  N P  ++LQ           KL  ++ 
Sbjct: 298  KNFITLFTGNETSETW----------FKAALAMNQPWSEKLQAVDNDVYRSLNKLRQIEE 347

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
            +  L +  ++DINR+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 348  ETGLTIEQVKDINRRMSIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 407

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 408  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 467

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
            +LQETG EP P  +A +M M E+KI K++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 468  MLQETGREPTPEELAERMLMSEDKIHKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIE 527

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+RS  K++L  LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 528  MPLDSATLDSLRSATKEVLAGLTAREAKVLRMRFGIGMTNDHTLEEVGKQFDVTRERIRQ 587

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FLE
Sbjct: 588  IEAKALRKLRHPSRSEVLRSFLE 610



 Score =  549 bits (1414), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 305/610 (50%), Positives = 404/610 (66%), Gaps = 36/610 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K+L+  GKE+GYLTF+E+ND LP+DI+D + IE II+    M I V E   D 
Sbjct: 3   QNQQSQLKLLVTHGKEQGYLTFAEVNDHLPDDIVDSDQIEDIIQMINDMGIRVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + L+L   T+ D  E+A EAA   LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+I
Sbjct: 63  DDLLLLADTNPDTDEDAVEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDI 122

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF-------SS 206
           AKRIE+G+  +  +++     I  +L   D++   E ++ +++ G +D +         +
Sbjct: 123 AKRIEDGINQVQCSVAEYLKAISYLLEQYDRVEAGEARLSDLITGFVDSSVVEEMMLAPT 182

Query: 207 NNRV-IKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEG 265
           N R  +  N+  +EE+    S   D S +    L  +   KF  +   ++  RK  +  G
Sbjct: 183 NVRSELATNEITDEEEHDEASKEDDNSIDP--GLARQ---KFVELREQYEMTRKVIKTNG 237

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            N          +S      R   K  + L + +R  + +V   E+ I+++ V+   MP+
Sbjct: 238 RNHTKSAAELMKLSTVFKQFRLIPKLFDYLVNNMRAMMTRVRTQERVIMKLCVDISKMPK 297

Query: 326 LHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ----------QKLINLQT 375
            +FI +F  NE +  W          +   L  N P  ++LQ           KL  ++ 
Sbjct: 298 KNFITLFTGNETSETW----------FKAALAMNQPWSEKLQAVDNDVYRSLNKLRQIEE 347

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
           +  L +  ++DINR+M  GE KAR+AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 348 ETGLTIEQVKDINRRMSIGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 407

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 408 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 467

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
           +LQETG EP P  +A +M M E+KI K++KIAKEP+SME+P+GDDEDSHLGDFIED  + 
Sbjct: 468 MLQETGREPTPEELAERMLMSEDKIHKVLKIAKEPISMETPIGDDEDSHLGDFIEDNTIE 527

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+RS  K++L  LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 528 MPLDSATLDSLRSATKEVLAGLTAREAKVLRMRFGIGMTNDHTLEEVGKQFDVTRERIRQ 587

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 588 IEAKALRKLR 597


>gi|424742631|ref|ZP_18170953.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-141]
 gi|422944247|gb|EKU39252.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-141]
          Length = 623

 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 298/615 (48%), Positives = 417/615 (67%), Gaps = 26/615 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 11   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 70

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
             T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71   DTADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------------------- 994
            ++++I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 131  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEDAP 190

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 1054
            ++  + +K + +  +E+   +  S   S    E  K    ++F+ +   + K +   EK 
Sbjct: 191  ATPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAK----VRFNELESAWTKTKAVIEKH 246

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M 
Sbjct: 247  GRNSPEADEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMD 306

Query: 1115 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            R  F   FP+ E N  W+D +  K   +  + L +  P +   QQK+ +++ ++ L + +
Sbjct: 307  RTQFRTSFPKQESNPAWLDEQIAKAPAEIKVHLEKVRPDVLAFQQKIADIEKELSLSVAE 366

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 367  IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 426

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 427  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 486

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +
Sbjct: 487  PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATS 546

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 547  EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 606

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FLE
Sbjct: 607  LRHPSRSEHLRSFLE 621



 Score =  548 bits (1412), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 290/602 (48%), Positives = 408/602 (67%), Gaps = 26/602 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 11  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 70

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
            T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71  DTADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------------------- 204
           ++++I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 131 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEDAP 190

Query: 205 SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE 264
           ++  + +K + +  +E+   +  S   S    E  K    ++F+ +   + K +   EK 
Sbjct: 191 ATPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAK----VRFNELESAWTKTKAVIEKH 246

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M 
Sbjct: 247 GRNSPEADEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMD 306

Query: 325 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           R  F   FP+ E N  W+D +  K   +  + L +  P +   QQK+ +++ ++ L + +
Sbjct: 307 RTQFRTSFPKQESNPAWLDEQIAKAPAEIKVHLEKVRPDVLAFQQKIADIEKELSLSVAE 366

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 367 IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 426

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 427 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 486

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +
Sbjct: 487 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATS 546

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 547 EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 606

Query: 624 LR 625
           LR
Sbjct: 607 LR 608


>gi|389721482|ref|ZP_10188234.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter sp. HA]
 gi|388608778|gb|EIM37974.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter sp. HA]
          Length = 628

 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 295/613 (48%), Positives = 407/613 (66%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  GKE+GYLTF+E+ND LP+ I + E IE II+    + I V +   +++  M  +  
Sbjct: 14   LISRGKEQGYLTFAEVNDHLPDSITESEQIEDIIQMLNDVGIPVHDRAPESDDAMFEDTA 73

Query: 896  SDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
               D     EAA    +V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKGNKNNNEEKI 1012
            ++H+I+  P  +  +L         E ++ +++ G +D     +   V++   +  E++ 
Sbjct: 134  VLHSIAYWPNAVEVVLQEYKDYEAGERRLADLLSGYLDPETDDDIPEVLEEVADIEEDEE 193

Query: 1013 LIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGY 1056
                S+ D+  +  E  +                  + ++F+ +S  +   +   EK G 
Sbjct: 194  ATTKSTKDVKLDDEEDEEESDSDDDSEGDSGPDPEIAKVRFAELSDAWKNTKAVIEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS+    A   ++   +  +FT +  + + + +R   +Q+   E++++   V +  M R 
Sbjct: 254  NSKEAEDALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRSAEREVMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D++
Sbjct: 314  QFRTSFPGQESNPAWLDEQIAKAPADQKAYLEKVRPDVLAFQQKIADIEKELDLKVRDIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  548 bits (1412), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 287/600 (47%), Positives = 398/600 (66%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  GKE+GYLTF+E+ND LP+ I + E IE II+    + I V +   +++  M  +  
Sbjct: 14  LISRGKEQGYLTFAEVNDHLPDSITESEQIEDIIQMLNDVGIPVHDRAPESDDAMFEDTA 73

Query: 106 SDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
              D     EAA    +V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKGNKNNNEEKI 222
           ++H+I+  P  +  +L         E ++ +++ G +D     +   V++   +  E++ 
Sbjct: 134 VLHSIAYWPNAVEVVLQEYKDYEAGERRLADLLSGYLDPETDDDIPEVLEEVADIEEDEE 193

Query: 223 LIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGY 266
               S+ D+  +  E  +                  + ++F+ +S  +   +   EK G 
Sbjct: 194 ATTKSTKDVKLDDEEDEEESDSDDDSEGDSGPDPEIAKVRFAELSDAWKNTKAVIEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS+    A   ++   +  +FT +  + + + +R   +Q+   E++++   V +  M R 
Sbjct: 254 NSKEAEDALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRSAEREVMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D++
Sbjct: 314 QFRTSFPGQESNPAWLDEQIAKAPADQKAYLEKVRPDVLAFQQKIADIEKELDLKVRDIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|169632612|ref|YP_001706348.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii SDF]
 gi|169151404|emb|CAP00133.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
            during exponential growth [Acinetobacter baumannii]
          Length = 630

 Score =  564 bits (1454), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 296/615 (48%), Positives = 418/615 (67%), Gaps = 22/615 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++++I+  P  +  +L   +     E ++ +I+ G +D    ++  + +  ++  E +  
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETETDEDIPEVLEDVEELEEE 193

Query: 1014 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 1054
             ESS+      +L+    E                   + ++F+ +   + + +   EK 
Sbjct: 194  DESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKH 253

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M 
Sbjct: 254  GRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMD 313

Query: 1115 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            R  F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++
Sbjct: 314  RNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSE 373

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 374  IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 433

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 434  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 493

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +
Sbjct: 494  PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATS 553

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 554  KGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 613

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FLE
Sbjct: 614  LRHPSRSEHLRSFLE 628



 Score =  548 bits (1412), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 288/602 (47%), Positives = 409/602 (67%), Gaps = 22/602 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++++I+  P  +  +L   +     E ++ +I+ G +D    ++  + +  ++  E +  
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETETDEDIPEVLEDVEELEEE 193

Query: 224 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 264
            ESS+      +L+    E                   + ++F+ +   + + +   EK 
Sbjct: 194 DESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKH 253

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M 
Sbjct: 254 GRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMD 313

Query: 325 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           R  F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++
Sbjct: 314 RNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSE 373

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 374 IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 433

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 434 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 493

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +
Sbjct: 494 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATS 553

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 554 KGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 613

Query: 624 LR 625
           LR
Sbjct: 614 LR 615


>gi|312883925|ref|ZP_07743642.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
            BAA-2122]
 gi|309368383|gb|EFP95918.1| RNA polymerase sigma factor RpoD [Vibrio caribbenthicus ATCC
            BAA-2122]
          Length = 618

 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 308/615 (50%), Positives = 411/615 (66%), Gaps = 13/615 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPNADETTAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 1053
              +   +  ++        ++ +    +           +L KF+++   F   + A  +
Sbjct: 183  IGSELTESELDDEDDVDDEDEEDGEGTDDEEESGIDPELALEKFTSLRNTFQNFQLACNE 242

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243  YGSESPKAQIAHELVLDVFREFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKM 302

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +  
Sbjct: 303  PKKSFITLFTGNESSDAWLDEILASDKPYAEKIRRSEDDIRRSIAKLKTIEEETSLTVQS 362

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363  IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483  PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543  GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 603  LRHPSRSETLRSFLD 617



 Score =  549 bits (1415), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 301/602 (50%), Positives = 402/602 (66%), Gaps = 13/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D N          +
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPNADETTAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 263
             +   +  ++        ++ +    +           +L KF+++   F   + A  +
Sbjct: 183 IGSELTESELDDEDDVDDEDEEDGEGTDDEEESGIDPELALEKFTSLRNTFQNFQLACNE 242

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243 YGSESPKAQIAHELVLDVFREFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKM 302

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +  
Sbjct: 303 PKKSFITLFTGNESSDAWLDEILASDKPYAEKIRRSEDDIRRSIAKLKTIEEETSLTVQS 362

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543 GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 624 LR 625
           LR
Sbjct: 603 LR 604


>gi|260548994|ref|ZP_05823216.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|424054507|ref|ZP_17792031.1| RNA polymerase sigma factor RpoD [Acinetobacter nosocomialis Ab22222]
 gi|425741402|ref|ZP_18859550.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-487]
 gi|260408162|gb|EEX01633.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|407439256|gb|EKF45781.1| RNA polymerase sigma factor RpoD [Acinetobacter nosocomialis Ab22222]
 gi|425492406|gb|EKU58665.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-487]
          Length = 628

 Score =  564 bits (1453), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/613 (47%), Positives = 413/613 (67%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
               K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194  SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP++E N  W+D +  K   +  + L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314  QFRTSFPKHESNPAWLDEQIAKAPAEIKVHLEKVRPDVLAFQQKIADIEKELNLSVAEIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  548 bits (1411), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 285/600 (47%), Positives = 404/600 (67%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
              K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194 SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP++E N  W+D +  K   +  + L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314 QFRTSFPKHESNPAWLDEQIAKAPAEIKVHLEKVRPDVLAFQQKIADIEKELNLSVAEIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|322513554|ref|ZP_08066654.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus ureae
            ATCC 25976]
 gi|322120625|gb|EFX92519.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinobacillus ureae
            ATCC 25976]
          Length = 618

 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 307/610 (50%), Positives = 410/610 (67%), Gaps = 25/610 (4%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 1013
             A++  P  + E++    ++ +  +++ ++V   +D N      V  ++   ++ + + +
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNAQEEATVEDLEAVLDDEDAEAV 193

Query: 1014 IE----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN---S 1058
             +           SSAD   +     +L  E   KF  +    +K  +A +K G     S
Sbjct: 194  ADVDDESEEEGSDSSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRGHKKS 250

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
               I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  F
Sbjct: 251  REQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADF 307

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            +K+F  NE +  W++     +      L   +  I+     L  ++    L +  +R+I 
Sbjct: 308  LKLFQGNETSEEWIEKAINAKKGAAPKLANYVDQIRVNIANLQRMEQSTGLTVAQIREIG 367

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 368  GRIANGELKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 427

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 428  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 487

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 488  LAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 547

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
               ++L  LTPRE KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 548  ATNEVLEGLTPREEKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 607

Query: 1419 RYYKLKIFLE 1428
            R   L+ FL+
Sbjct: 608  RSETLRSFLD 617



 Score =  548 bits (1413), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 300/597 (50%), Positives = 401/597 (67%), Gaps = 25/597 (4%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 223
            A++  P  + E++    ++ +  +++ ++V   +D N      V  ++   ++ + + +
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNAQEEATVEDLEAVLDDEDAEAV 193

Query: 224 IE----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN---S 268
            +           SSAD   +     +L  E   KF  +    +K  +A +K G     S
Sbjct: 194 ADVDDESEEEGSDSSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRGHKKS 250

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
              I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  F
Sbjct: 251 REQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADF 307

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           +K+F  NE +  W++     +      L   +  I+     L  ++    L +  +R+I 
Sbjct: 308 LKLFQGNETSEEWIEKAINAKKGAAPKLANYVDQIRVNIANLQRMEQSTGLTVAQIREIG 367

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
            ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 368 GRIANGELKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 427

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  
Sbjct: 428 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEE 487

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R 
Sbjct: 488 LAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRI 547

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              ++L  LTPRE KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 ATNEVLEGLTPREEKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|190150752|ref|YP_001969277.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
            serovar 7 str. AP76]
 gi|189915883|gb|ACE62135.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
            serovar 7 str. AP76]
          Length = 619

 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 413/611 (67%), Gaps = 26/611 (4%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 1015
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1016 SSS-------------ADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN--- 1057
             +              AD   +     +L  E   KF  +    +K  +A +K G +   
Sbjct: 194  VADVDDESEEEESDGSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRSHKK 250

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  
Sbjct: 251  SREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKAD 307

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K+F  NE +  W++     +      L   I  I+     L +++    L +  +R+I
Sbjct: 308  FLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREI 367

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
              ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 368  GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 427

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 428  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 487

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 488  ELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 547

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
                ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 548  LATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 607

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 608  SRSETLRSFLD 618



 Score =  548 bits (1413), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 404/598 (67%), Gaps = 26/598 (4%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 225
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 226 SSS-------------ADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN--- 267
            +              AD   +     +L  E   KF  +    +K  +A +K G +   
Sbjct: 194 VADVDDESEEEESDGSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRSHKK 250

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  
Sbjct: 251 SREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKAD 307

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K+F  NE +  W++     +      L   I  I+     L +++    L +  +R+I
Sbjct: 308 FLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREI 367

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 368 GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 427

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 428 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 487

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 488 ELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 547

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|425744936|ref|ZP_18862991.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-323]
 gi|425490532|gb|EKU56832.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-323]
          Length = 629

 Score =  563 bits (1452), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 307/618 (49%), Positives = 416/618 (67%), Gaps = 29/618 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------------------- 991
            ++H+I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEAEIEEEDEE 193

Query: 992  KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 1051
            K+ SS  + +K + ++ EE+   +  S   S    E  K    ++FS +   +++ +   
Sbjct: 194  KDSSSKAKDVKLDDDDEEEESEGDDDSEGDSGPDPEVAK----VRFSELEAAWNETKTVV 249

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             K G NSE    A   ++   +  +FT +  E + + +R    Q+   E++I+   V + 
Sbjct: 250  AKHGRNSEEAKAALEALAAVFMMFKFTPRLFEIISEMIRGTHEQIRSNEREIMRYAVRRG 309

Query: 1112 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             M R  F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ D+ L 
Sbjct: 310  RMDRNQFRTTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIENDLGLN 369

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + D+++I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 370  VKDIKEISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 429

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 430  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 489

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 490  GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDA 549

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 550  ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 609

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FLE
Sbjct: 610  LRKLRHPSRSEHLRSFLE 627



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 299/605 (49%), Positives = 407/605 (67%), Gaps = 29/605 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------------------- 201
           ++H+I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEAEIEEEDEE 193

Query: 202 KNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAF 261
           K+ SS  + +K + ++ EE+   +  S   S    E  K    ++FS +   +++ +   
Sbjct: 194 KDSSSKAKDVKLDDDDEEEESEGDDDSEGDSGPDPEVAK----VRFSELEAAWNETKTVV 249

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            K G NSE    A   ++   +  +FT +  E + + +R    Q+   E++I+   V + 
Sbjct: 250 AKHGRNSEEAKAALEALAAVFMMFKFTPRLFEIISEMIRGTHEQIRSNEREIMRYAVRRG 309

Query: 322 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            M R  F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ D+ L 
Sbjct: 310 RMDRNQFRTTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIENDLGLN 369

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + D+++I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 370 VKDIKEISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 429

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 430 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 489

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 490 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDA 549

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 550 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 609

Query: 621 LRKLR 625
           LRKLR
Sbjct: 610 LRKLR 614


>gi|307264154|ref|ZP_07545748.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 13 str. N273]
 gi|306870528|gb|EFN02278.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 13 str. N273]
          Length = 619

 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 413/611 (67%), Gaps = 26/611 (4%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 1015
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1016 SSS-------------ADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN--- 1057
             +              AD   +     +L  E   KF  +    +K  +A +K G +   
Sbjct: 194  VADVDDESEEEESDGSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRSHKK 250

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  
Sbjct: 251  SREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKAD 307

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            F+K+F  NE +  W++     +      L   I  I+     L +++    L +  +R+I
Sbjct: 308  FLKLFRGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREI 367

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
              ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 368  GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 427

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 428  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 487

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 488  ELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 547

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
                ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 548  LATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 607

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FL+
Sbjct: 608  SRSETLRSFLD 618



 Score =  548 bits (1412), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 404/598 (67%), Gaps = 26/598 (4%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 225
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 226 SSS-------------ADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYN--- 267
            +              AD   +     +L  E   KF  +    +K  +A +K G +   
Sbjct: 194 VADVDDESEEEESDGSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRSHKK 250

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M +  
Sbjct: 251 SREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKAD 307

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           F+K+F  NE +  W++     +      L   I  I+     L +++    L +  +R+I
Sbjct: 308 FLKLFRGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQHMEQTTGLTIAQIREI 367

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
             ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 368 GGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 427

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P 
Sbjct: 428 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPE 487

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R
Sbjct: 488 ELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLR 547

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 LATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|445434350|ref|ZP_21439963.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC021]
 gi|444756332|gb|ELW80877.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC021]
          Length = 628

 Score =  563 bits (1451), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/613 (47%), Positives = 411/613 (67%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELAEEDE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
               K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194  SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314  QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELNLSVAEIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  547 bits (1409), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 285/600 (47%), Positives = 402/600 (67%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELAEEDE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
              K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194 SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314 QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELNLSVAEIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|94676896|ref|YP_589041.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
            (Homalodisca coagulata)]
 gi|94220046|gb|ABF14205.1| RNA polymerase, sigma 70 factor [Baumannia cicadellinicola str. Hc
            (Homalodisca coagulata)]
          Length = 612

 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 301/612 (49%), Positives = 407/612 (66%), Gaps = 13/612 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N   + K+L+  GKE+GYLT +E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3    QNQHLQLKLLVTRGKEQGYLTVAEVNDLLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 887  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            + ++L    SD D E+A EAA   LS+V+S+  RT DP++MYMREMG+VELLTR+GEI I
Sbjct: 63   DDILLDETNSDTD-EDAVEAAAQVLSSVESEIVRTTDPVRMYMREMGTVELLTREGEINI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++   +D +    +  I  
Sbjct: 122  AKRIEDGMTQVQCSVAEYPEAITYLLKQYDRVELGEARLSDLIINFVDTHMEVPD--IIS 179

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGY 1056
              +N   ++  + S  +      E    +S I       KF  +   ++  R   + +G 
Sbjct: 180  TTSNISTELASDISDDEDEEVNDENTNEDSSIDPEIAHQKFVELREQYEITRNIIDTKGR 239

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +    I+    +S          K  + L   +R  ++++   E+ ++++ V+   MP+ 
Sbjct: 240  SHAKAIEEILKLSEIFKQFHLAPKQFDYLVKNMRAVMDRIRLQERLVMKLCVDISKMPKK 299

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FIK+F  NE +  W      +   ++  L     ++    QKL  ++ +  L +  ++D
Sbjct: 300  DFIKLFAGNETSETWFKTALAMNQPWSEKLYNVDKNVHNSLQKLRQIEEETGLSIEQIKD 359

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 360  INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 419

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 420  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTP 479

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDDED+HLGDFIED  +  P ++A + S+
Sbjct: 480  EELAERMFMPEDKIRKVLKIAKEPLSMETPIGDDEDTHLGDFIEDTTLELPLESATSESL 539

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            RS   +IL  LT RE+KVLRMRFGI+M++DHTLEEVGKQF VTRERIRQIEAKALRKLRH
Sbjct: 540  RSATHEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFAVTRERIRQIEAKALRKLRH 599

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 600  PSRSEVLRSFLD 611



 Score =  548 bits (1413), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 294/599 (49%), Positives = 398/599 (66%), Gaps = 13/599 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N   + K+L+  GKE+GYLT +E+ND LPEDI+D + IE II+    M I V E   D 
Sbjct: 3   QNQHLQLKLLVTRGKEQGYLTVAEVNDLLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDA 62

Query: 97  ETLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           + ++L    SD D E+A EAA   LS+V+S+  RT DP++MYMREMG+VELLTR+GEI I
Sbjct: 63  DDILLDETNSDTD-EDAVEAAAQVLSSVESEIVRTTDPVRMYMREMGTVELLTREGEINI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE+G+  +  +++  P  I  +L   D++   E ++ +++   +D +    +  I  
Sbjct: 122 AKRIEDGMTQVQCSVAEYPEAITYLLKQYDRVELGEARLSDLIINFVDTHMEVPD--IIS 179

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYESLI-------KFSNISFHFDKMRKAFEKEGY 266
             +N   ++  + S  +      E    +S I       KF  +   ++  R   + +G 
Sbjct: 180 TTSNISTELASDISDDEDEEVNDENTNEDSSIDPEIAHQKFVELREQYEITRNIIDTKGR 239

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +    I+    +S          K  + L   +R  ++++   E+ ++++ V+   MP+ 
Sbjct: 240 SHAKAIEEILKLSEIFKQFHLAPKQFDYLVKNMRAVMDRIRLQERLVMKLCVDISKMPKK 299

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FIK+F  NE +  W      +   ++  L     ++    QKL  ++ +  L +  ++D
Sbjct: 300 DFIKLFAGNETSETWFKTALAMNQPWSEKLYNVDKNVHNSLQKLRQIEEETGLSIEQIKD 359

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           INR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 360 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 419

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 420 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTP 479

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDDED+HLGDFIED  +  P ++A + S+
Sbjct: 480 EELAERMFMPEDKIRKVLKIAKEPLSMETPIGDDEDTHLGDFIEDTTLELPLESATSESL 539

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RS   +IL  LT RE+KVLRMRFGI+M++DHTLEEVGKQF VTRERIRQIEAKALRKLR
Sbjct: 540 RSATHEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFAVTRERIRQIEAKALRKLR 598


>gi|32034495|ref|ZP_00134667.1| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208939|ref|YP_001054164.1| RNA polymerase sigma factor RpoD [Actinobacillus pleuropneumoniae
            serovar 5b str. L20]
 gi|307257544|ref|ZP_07539308.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 10 str. D13039]
 gi|126097731|gb|ABN74559.1| RNA polymerase sigma factor 70 [Actinobacillus pleuropneumoniae
            serovar 5b str. L20]
 gi|306863980|gb|EFM95899.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 10 str. D13039]
          Length = 619

 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 412/612 (67%), Gaps = 28/612 (4%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 1015
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1016 ----------------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN-- 1057
                            + + D ++   E  +     KF  +    +K  +A +K G +  
Sbjct: 194  VADVDDESEEEESDGSTDTGDDNSIDPELARE----KFYALREQHEKALQAIQKHGRSHK 249

Query: 1058 -SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
             S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M + 
Sbjct: 250  KSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKA 306

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+K+F  NE +  W++     +      L   I  I+     L  ++    L +  +R+
Sbjct: 307  DFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIRE 366

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 367  IGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 426

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P
Sbjct: 427  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATP 486

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+
Sbjct: 487  EELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESL 546

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 547  RLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FL+
Sbjct: 607  PSRSETLRSFLD 618



 Score =  548 bits (1411), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 403/599 (67%), Gaps = 28/599 (4%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIE 225
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +   + + ++E+   +
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 226 ----------------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN-- 267
                           + + D ++   E  +     KF  +    +K  +A +K G +  
Sbjct: 194 VADVDDESEEEESDGSTDTGDDNSIDPELARE----KFYALREQHEKALQAIQKHGRSHK 249

Query: 268 -SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
            S   I+A ++I  E    R   K  + L ++++  + QV   E+QI    V    M + 
Sbjct: 250 KSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQRYAVEYAQMKKA 306

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+K+F  NE +  W++     +      L   I  I+     L  ++    L +  +R+
Sbjct: 307 DFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQTTGLTIAQIRE 366

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 367 IGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 426

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P
Sbjct: 427 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATP 486

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+
Sbjct: 487 EELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESL 546

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 547 RLATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|407693701|ref|YP_006818490.1| RNA polymerase sigma factor RpoD [Actinobacillus suis H91-0380]
 gi|407389758|gb|AFU20251.1| RNA polymerase sigma factor RpoD [Actinobacillus suis H91-0380]
          Length = 618

 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/607 (49%), Positives = 408/607 (67%), Gaps = 19/607 (3%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 1013
             A++  P  + E++    ++ +  +++ ++V   +D N      V  ++   ++ + + +
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNAQEEATVEDLEAVLDDEDAEAV 193

Query: 1014 IE----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
             +           SSAD   +     +L  E   KF  +    +K  +A +K G   +  
Sbjct: 194  ADVDDESEEEEGDSSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRGHKKS 250

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             +    +S+     R   K  + L ++++  + QV   E+QI    V    M +  F+K+
Sbjct: 251  REQIQVLSDIFREFRLVPKQFDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADFLKL 310

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE +  W++     +      L   +  I+     L  ++    L +  +R+I  ++
Sbjct: 311  FQGNETSEEWIEKAINAKKGAAPKLANYVDQIRVNIANLQRMEQSTGLTVAQIREIGGRI 370

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 371  ANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 430

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A 
Sbjct: 431  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAE 490

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    
Sbjct: 491  RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATN 550

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 551  EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 610

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 611  TLRSFLD 617



 Score =  548 bits (1411), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 296/594 (49%), Positives = 399/594 (67%), Gaps = 19/594 (3%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKIL 223
            A++  P  + E++    ++ +  +++ ++V   +D N      V  ++   ++ + + +
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNAQEEATVEDLEAVLDDEDAEAV 193

Query: 224 IE----------SSSADLSTEQL--EKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
            +           SSAD   +     +L  E   KF  +    +K  +A +K G   +  
Sbjct: 194 ADVDDESEEEEGDSSADTGDDNSIDPELARE---KFYALREQHEKALQAIQKHGRGHKKS 250

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            +    +S+     R   K  + L ++++  + QV   E+QI    V    M +  F+K+
Sbjct: 251 REQIQVLSDIFREFRLVPKQFDLLVESMQKMMKQVRAEERQIQRYAVEYAQMKKADFLKL 310

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE +  W++     +      L   +  I+     L  ++    L +  +R+I  ++
Sbjct: 311 FQGNETSEEWIEKAINAKKGAAPKLANYVDQIRVNIANLQRMEQSTGLTVAQIREIGGRI 370

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 371 ANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 430

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQE G E  P  +A 
Sbjct: 431 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQEMGREATPEELAE 490

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++  P D+A   S+R    
Sbjct: 491 RMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLELPLDSATAESLRIATN 550

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 EVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|444920304|ref|ZP_21240147.1| RNA polymerase sigma factor rpoD [Wohlfahrtiimonas chitiniclastica
            SH04]
 gi|444508623|gb|ELV08792.1| RNA polymerase sigma factor rpoD [Wohlfahrtiimonas chitiniclastica
            SH04]
          Length = 627

 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 306/639 (47%), Positives = 427/639 (66%), Gaps = 32/639 (5%)

Query: 808  FSKKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIES 867
             SK+NA +          ++  + + K LI  GKE+GYLT++EIND LPEDIID E IES
Sbjct: 1    MSKQNALT----------VKEQQARIKELIAQGKEQGYLTYAEINDHLPEDIIDPEQIES 50

Query: 868  IIKTFRYMDISVSEHVLDTETLMLSN--ITSDDDVEEATEAALSTVDS-DFGRTKDPIKM 924
            II     M I VS+   D ++L+L+N  I SDDD  +   A L  +DS + GRT DP++M
Sbjct: 51   IIAMISEMGIKVSDEAPDMDSLLLTNDSIGSDDDAVDEAAAVLVNIDSSEIGRTTDPVRM 110

Query: 925  YMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDE 984
            YMREMG+V+LL+RD E  IA RIEEGL   +  +++    +  ++   ++  + + ++ +
Sbjct: 111  YMREMGTVDLLSRDEEKSIAIRIEEGLNSALLNLANYYPAVDLLIARYEETLETDQRLGD 170

Query: 985  IVDGLIDKNFSSNNRVIKGNKNNNEEKILIE---------------SSSADLSTEQLEKL 1029
            I  G +D ++ S    I  +K++ E +I+ +                S+A   T   +++
Sbjct: 171  IATGFVDPSYYSE---IAEDKDDEELEIVDDEAPADDLEDDEESEGGSAASAETGPNKEI 227

Query: 1030 KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
              E + +   I    D +R    K+  ++   + A   + ++ +  R   K  E +   L
Sbjct: 228  FAEKIAELKAIIAEIDALRGNKRKKNIDA-LILDAQERLKSKFIEFRLAPKMQEDMVALL 286

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            +  I+++  +E+++++I +  C MPR  FIK FP NE    WV+     +H Y   +  +
Sbjct: 287  KETIDRIRPLERKMMKICIATCKMPRDAFIKTFPRNETKKEWVEEVINSKHKYAKAIEEH 346

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
              +I E+Q +L  ++    L + ++++INR++   E KA++AKREM EANLRLVISIAKK
Sbjct: 347  KDAIFEIQTQLAKIEKANSLAIYEIKEINREISINEAKAKRAKREMIEANLRLVISIAKK 406

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 407  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIP 466

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQ+LQ+ G E  P  +A  M +PE++IRK++KIAKEP+SME+PVGD
Sbjct: 467  VHMIETINKLNRISRQMLQDMGREATPEELAEAMGLPEDRIRKVLKIAKEPISMETPVGD 526

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            DEDSHLGDFIED  M++P +AA +  +    +++L +LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 527  DEDSHLGDFIEDTGMVSPLEAATSVGLSEATREVLETLTPREAKVLRMRFGIDMNTDHTL 586

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ F++
Sbjct: 587  EEVGKQFDVTRERIRQIEAKALRKLRHPNRSESLRSFMD 625



 Score =  549 bits (1414), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 297/602 (49%), Positives = 409/602 (67%), Gaps = 22/602 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++EIND LPEDIID E IESII     M I VS+   D ++L+L
Sbjct: 15  RIKELIAQGKEQGYLTYAEINDHLPEDIIDPEQIESIIAMISEMGIKVSDEAPDMDSLLL 74

Query: 102 SN--ITSDDDVEEATEAALSTVDS-DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
           +N  I SDDD  +   A L  +DS + GRT DP++MYMREMG+V+LL+RD E  IA RIE
Sbjct: 75  TNDSIGSDDDAVDEAAAVLVNIDSSEIGRTTDPVRMYMREMGTVDLLSRDEEKSIAIRIE 134

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNN 218
           EGL   +  +++    +  ++   ++  + + ++ +I  G +D ++ S    I  +K++ 
Sbjct: 135 EGLNSALLNLANYYPAVDLLIARYEETLETDQRLGDIATGFVDPSYYSE---IAEDKDDE 191

Query: 219 EEKILIE---------------SSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
           E +I+ +                S+A   T   +++  E + +   I    D +R    K
Sbjct: 192 ELEIVDDEAPADDLEDDEESEGGSAASAETGPNKEIFAEKIAELKAIIAEIDALRGNKRK 251

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
           +  ++   + A   + ++ +  R   K  E +   L+  I+++  +E+++++I +  C M
Sbjct: 252 KNIDA-LILDAQERLKSKFIEFRLAPKMQEDMVALLKETIDRIRPLERKMMKICIATCKM 310

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           PR  FIK FP NE    WV+     +H Y   +  +  +I E+Q +L  ++    L + +
Sbjct: 311 PRDAFIKTFPRNETKKEWVEEVINSKHKYAKAIEEHKDAIFEIQTQLAKIEKANSLAIYE 370

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           +++INR++   E KA++AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 371 IKEINREISINEAKAKRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 430

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E
Sbjct: 431 KFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQDMGRE 490

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
             P  +A  M +PE++IRK++KIAKEP+SME+PVGDDEDSHLGDFIED  M++P +AA +
Sbjct: 491 ATPEELAEAMGLPEDRIRKVLKIAKEPISMETPVGDDEDSHLGDFIEDTGMVSPLEAATS 550

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             +    +++L +LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 551 VGLSEATREVLETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 610

Query: 624 LR 625
           LR
Sbjct: 611 LR 612


>gi|157374211|ref|YP_001472811.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
            HAW-EB3]
 gi|157316585|gb|ABV35683.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
            HAW-EB3]
          Length = 612

 Score =  563 bits (1450), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 301/601 (50%), Positives = 404/601 (67%), Gaps = 4/601 (0%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 11   QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S  ++D+D  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDSTDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 1007
              +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   V     + 
Sbjct: 131  NTVQASVAEYPQAISMILEQFDRYEAEEVRLSDIISGFVDPNADDVAPTATHVGSELSDE 190

Query: 1008 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
              +    E    +           E+  +F+ +    +   K    +G        A   
Sbjct: 191  ELDDEDDEEDDDEEEEGPKGPDPEEAKERFTQLREVHENTLKVIALKGRGHPESTLALFE 250

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+KV+  NE 
Sbjct: 251  IGELFKEFRLMPKQFDRLVKNMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNES 310

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            ++ W + E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M  GE K
Sbjct: 311  SIEWFNEELASKKPYVEGLEMVDPDVRRCRAKLDAIEKETGLAIASIKDINRRMSIGEAK 370

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 371  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE
Sbjct: 431  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPE 490

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++L  L
Sbjct: 491  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGL 550

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK FL
Sbjct: 551  TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILKSFL 610

Query: 1428 E 1428
            +
Sbjct: 611  D 611



 Score =  548 bits (1412), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 293/588 (49%), Positives = 395/588 (67%), Gaps = 4/588 (0%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE I++    M I V E   D + +M+
Sbjct: 11  QLKLLLAKGKEQGYLTYAEVNDHLPADMVDADQIEDIVQMINDMGIRVYEQAPDADEIMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S  ++D+D  E   AAL+TV+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDSTDEDAAEEAAAALATVEAELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRVIKGNKNN 217
             +  +++  P  I  IL   D+    E+++ +I+ G +D N      +   V     + 
Sbjct: 131 NTVQASVAEYPQAISMILEQFDRYEAEEVRLSDIISGFVDPNADDVAPTATHVGSELSDE 190

Query: 218 NEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
             +    E    +           E+  +F+ +    +   K    +G        A   
Sbjct: 191 ELDDEDDEEDDDEEEEGPKGPDPEEAKERFTQLREVHENTLKVIALKGRGHPESTLALFE 250

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           I       R   K  ++L   +R  +++V   E+ I+++ V +  MP+ +F+KV+  NE 
Sbjct: 251 IGELFKEFRLMPKQFDRLVKNMRAMMDKVRVQERLIMKLCVEQAKMPKKNFVKVYTSNES 310

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           ++ W + E   +  Y   L    P ++  + KL  ++ +  L +  ++DINR+M  GE K
Sbjct: 311 SIEWFNEELASKKPYVEGLEMVDPDVRRCRAKLDAIEKETGLAIASIKDINRRMSIGEAK 370

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 371 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 430

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M MPE
Sbjct: 431 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAERMLMPE 490

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++   ++L  L
Sbjct: 491 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATGESLKNATHEVLAGL 550

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 598


>gi|262371919|ref|ZP_06065198.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
 gi|262311944|gb|EEY93029.1| RNA polymerase sigma factor sigma-70 [Acinetobacter junii SH205]
          Length = 627

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 298/615 (48%), Positives = 411/615 (66%), Gaps = 25/615 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L   +     E ++ +I+ G +D     +   I            
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDDD---IPEVLEEEAVLED 190

Query: 1014 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 1054
             E+ +A     +L+    +                   + ++F+ +   ++  +   EK 
Sbjct: 191  AETPAAPAKDVKLDDDDEDEDSEGDDDSEGDSGPDPEVAKVRFTELESAWNDTKAIIEKH 250

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G +SE    A  +++   +  +FT +  + + + +R   +Q+   E++I+   V +  M 
Sbjct: 251  GRSSEEAKAALESLAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMD 310

Query: 1115 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            R  F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +
Sbjct: 311  RNQFRTTFPEQESNPAWLDEQIAKAPAEIKPHLEKVRPDVLAFQQKIADIEKELDLNVKE 370

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 371  IKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 430

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 431  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 490

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +
Sbjct: 491  PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATS 550

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 551  EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 610

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FLE
Sbjct: 611  LRHPSRSEHLRSFLE 625



 Score =  546 bits (1407), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 290/602 (48%), Positives = 402/602 (66%), Gaps = 25/602 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L   +     E ++ +I+ G +D     +   I            
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDDD---IPEVLEEEAVLED 190

Query: 224 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 264
            E+ +A     +L+    +                   + ++F+ +   ++  +   EK 
Sbjct: 191 AETPAAPAKDVKLDDDDEDEDSEGDDDSEGDSGPDPEVAKVRFTELESAWNDTKAIIEKH 250

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G +SE    A  +++   +  +FT +  + + + +R   +Q+   E++I+   V +  M 
Sbjct: 251 GRSSEEAKAALESLAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMD 310

Query: 325 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           R  F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +
Sbjct: 311 RNQFRTTFPEQESNPAWLDEQIAKAPAEIKPHLEKVRPDVLAFQQKIADIEKELDLNVKE 370

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 371 IKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 430

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 431 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 490

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +
Sbjct: 491 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATS 550

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 551 EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 610

Query: 624 LR 625
           LR
Sbjct: 611 LR 612


>gi|333369298|ref|ZP_08461425.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
            1501(2011)]
 gi|332974186|gb|EGK11120.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
            1501(2011)]
          Length = 624

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 289/616 (46%), Positives = 419/616 (68%), Gaps = 24/616 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +   LI++GKE+GYLT++E+ND LP  I + + IE I++    + I + E   D + +++
Sbjct: 12   QLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 892  SNITSDDDVE-EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            ++  +DD++  +   A L+ V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72   NDGANDDEMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
            ++D+ HA++  P T+  IL   D +   E K+ +++ G +D        V      ++EE
Sbjct: 132  IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVITGFLDPEEIEPPVV-----EDDEE 186

Query: 1011 KILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFDKMRKAFE 1052
            ++ + ++ + +     E  + E                     +   I   F   ++A E
Sbjct: 187  QLPVITTKSKVKELDDEDEEEEETDEEEDAEEAGGLDPELVRQRVEEIRELFATAKQALE 246

Query: 1053 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 1112
            + G  S    +A+  +++  + ++   +  + +   + +  + V + E+QI+ +V+ +  
Sbjct: 247  EYGRGSPQAEEAYAQLADRFMLLKLNNRMSDNVMAIMHDVYDDVRKQERQIMRLVIRRGK 306

Query: 1113 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
            MPR  F K FP NE N++W+ +  K    +   L + +  +  LQ+++ + +  + + + 
Sbjct: 307  MPRAEFRKTFPSNETNVDWLTDRLKGNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMEIG 366

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++++ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 367  EMKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 426

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G 
Sbjct: 427  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGR 486

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P + A 
Sbjct: 487  EPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDAT 546

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            +A ++   +D+L++LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 547  SAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 606

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FLE
Sbjct: 607  KLRHPSRSEHLRSFLE 622



 Score =  546 bits (1407), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 281/603 (46%), Positives = 410/603 (67%), Gaps = 24/603 (3%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +   LI++GKE+GYLT++E+ND LP  I + + IE I++    + I + E   D + +++
Sbjct: 12  QLATLIQMGKEQGYLTYAEVNDQLPASITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 102 SNITSDDDVE-EATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           ++  +DD++  +   A L+ V+++ GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72  NDGANDDEMATDEAAAVLAAVETEPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
           ++D+ HA++  P T+  IL   D +   E K+ +++ G +D        V      ++EE
Sbjct: 132 IRDVQHAMAYWPGTVQFILDEYDLVEAGEKKLSDVITGFLDPEEIEPPVV-----EDDEE 186

Query: 221 KILIESSSADLSTEQLEKLKYESLI------------------KFSNISFHFDKMRKAFE 262
           ++ + ++ + +     E  + E                     +   I   F   ++A E
Sbjct: 187 QLPVITTKSKVKELDDEDEEEEETDEEEDAEEAGGLDPELVRQRVEEIRELFATAKQALE 246

Query: 263 KEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCG 322
           + G  S    +A+  +++  + ++   +  + +   + +  + V + E+QI+ +V+ +  
Sbjct: 247 EYGRGSPQAEEAYAQLADRFMLLKLNNRMSDNVMAIMHDVYDDVRKQERQIMRLVIRRGK 306

Query: 323 MPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
           MPR  F K FP NE N++W+ +  K    +   L + +  +  LQ+++ + +  + + + 
Sbjct: 307 MPRAEFRKTFPSNETNVDWLTDRLKGNPKFADSLAKVVDDVVVLQRRIRDHEDKLDMEIG 366

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++++ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 367 EMKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 426

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G 
Sbjct: 427 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGR 486

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+ + +P + A 
Sbjct: 487 EPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQTISSPVEDAT 546

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           +A ++   +D+L++LT RE+KVLRMRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 547 SAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 606

Query: 623 KLR 625
           KLR
Sbjct: 607 KLR 609


>gi|171320298|ref|ZP_02909351.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria MEX-5]
 gi|171094445|gb|EDT39506.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria MEX-5]
          Length = 338

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 264/337 (78%), Positives = 304/337 (90%)

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            +++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RNIP+
Sbjct: 1    MDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRNIPA 60

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 61   IREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 120

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 121  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 180

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 181  IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 240

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 241  SHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 300

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            GKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 301  GKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 337



 Score =  541 bits (1393), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 253/323 (78%), Positives = 293/323 (90%)

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           +++V Q+E+QIL IVV+KCGMPR  FI  FP +E +L+W +      H Y+ +L RNIP+
Sbjct: 1   MDEVRQVERQILHIVVDKCGMPRSEFIARFPGSETDLDWAEKIAAEGHSYSAVLSRNIPA 60

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVISIAKKYT+
Sbjct: 61  IREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIAKKYTN 120

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 121 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 180

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+P+GDD+D
Sbjct: 181 IETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMETPIGDDDD 240

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+DHTLEEV
Sbjct: 241 SHLGDFIEDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEV 300

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 301 GKQFDVTRERIRQIEAKALRKLR 323


>gi|119773960|ref|YP_926700.1| RNA polymerase sigma-70 factor [Shewanella amazonensis SB2B]
 gi|119766460|gb|ABL99030.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella amazonensis SB2B]
          Length = 620

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 303/624 (48%), Positives = 407/624 (65%), Gaps = 42/624 (6%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11   QLKMLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEEAPDADEMMM 70

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71   SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
              +  +++  P  I  IL   D+   + I++ +               +I G  + NEE 
Sbjct: 131  NTVQSSVAEYPQAISMILEQFDQFEADAIRLSD---------------IISGFVDPNEED 175

Query: 1012 ILIESSSADLSTEQLEKLKYESLI---------------------------KFSNISFHF 1044
            +   ++       + E    + +                            +F+ +   +
Sbjct: 176  VGPTATHIGSELSEEELEDEDDMDEDEEEDEDGDSSDDDGAKGPDPEVARERFAALRAAY 235

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            D   K  E +G       +A   +       R   K  ++L  ++R  +++V   E+ I+
Sbjct: 236  DNALKVIEVKGRAHPESTRALFELGEIFKEFRLVPKQFDRLVKSMREMMDKVRVQERLIM 295

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            ++ V +  MP+ +F+K+F  NE +L W + E +    Y+  L      ++  + KL  ++
Sbjct: 296  KLCVEQAKMPKKNFVKLFTGNETDLTWFNKEIEAGRPYSADLKLVDEDVQRCRAKLEAIE 355

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 356  VETGLSIESIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 415

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 416  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 475

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 476  QMLQEMGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL 535

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
              P D+A + S++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 536  ELPLDSATSESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 595

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHPSR   LK FL+
Sbjct: 596  QIEAKALRKLRHPSRSEILKSFLD 619



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 295/611 (48%), Positives = 398/611 (65%), Gaps = 42/611 (6%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++E+ND LP D++D + IE II+    M I V E   D + +M+
Sbjct: 11  QLKMLLAKGKEQGYLTYAEVNDHLPADMVDSDQIEDIIQMINDMGIRVYEEAPDADEMMM 70

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           S   +D+D  E   AAL+TV+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG+
Sbjct: 71  SEDNTDEDAAEEAAAALATVESELGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEEGI 130

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
             +  +++  P  I  IL   D+   + I++ +               +I G  + NEE 
Sbjct: 131 NTVQSSVAEYPQAISMILEQFDQFEADAIRLSD---------------IISGFVDPNEED 175

Query: 222 ILIESSSADLSTEQLEKLKYESLI---------------------------KFSNISFHF 254
           +   ++       + E    + +                            +F+ +   +
Sbjct: 176 VGPTATHIGSELSEEELEDEDDMDEDEEEDEDGDSSDDDGAKGPDPEVARERFAALRAAY 235

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           D   K  E +G       +A   +       R   K  ++L  ++R  +++V   E+ I+
Sbjct: 236 DNALKVIEVKGRAHPESTRALFELGEIFKEFRLVPKQFDRLVKSMREMMDKVRVQERLIM 295

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           ++ V +  MP+ +F+K+F  NE +L W + E +    Y+  L      ++  + KL  ++
Sbjct: 296 KLCVEQAKMPKKNFVKLFTGNETDLTWFNKEIEAGRPYSADLKLVDEDVQRCRAKLEAIE 355

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  L +  ++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 356 VETGLSIESIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 415

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 416 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 475

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +A +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +
Sbjct: 476 QMLQEMGREPSPEELAERMAMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTL 535

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
             P D+A + S++    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 536 ELPLDSATSESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 595

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 596 QIEAKALRKLR 606


>gi|323495834|ref|ZP_08100902.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
 gi|323319050|gb|EGA71993.1| RNA polymerase sigma factor RpoD [Vibrio sinaloensis DSM 21326]
          Length = 620

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 312/617 (50%), Positives = 411/617 (66%), Gaps = 15/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKLLVLKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L      +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRV 1000
            KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +     +     
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1001 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAF 1051
            I      +E K        D   +  +    E         +L KF+++   F   + A 
Sbjct: 183  IGSELAESELKDEDAEDVEDEEEDGEDDDDSEEDTGIDPEFALEKFTSLRNTFQNFQLAC 242

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             + G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V   
Sbjct: 243  NEYGNESPKAQIAHELVLDVFKEFRLTPKQFDYLVNELRTSMERVRTQERLIMKASVEYG 302

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +
Sbjct: 303  KMPKKSFISLFSGNESSDAWLDEILASDKPYADKIRRSEDDIRRSIMKLKMIEEETSLTV 362

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
              ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363  QSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483  REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 542

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543  TATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 603  RKLRHPSRSETLRSFLD 619



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 305/604 (50%), Positives = 402/604 (66%), Gaps = 15/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K+L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKLLVLKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L      +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF----SSNNRV 210
           KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +     +     
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 211 IKGNKNNNEEKILIESSSADLSTEQLEKLKYE---------SLIKFSNISFHFDKMRKAF 261
           I      +E K        D   +  +    E         +L KF+++   F   + A 
Sbjct: 183 IGSELAESELKDEDAEDVEDEEEDGEDDDDSEEDTGIDPEFALEKFTSLRNTFQNFQLAC 242

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            + G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V   
Sbjct: 243 NEYGNESPKAQIAHELVLDVFKEFRLTPKQFDYLVNELRTSMERVRTQERLIMKASVEYG 302

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +
Sbjct: 303 KMPKKSFISLFSGNESSDAWLDEILASDKPYADKIRRSEDDIRRSIMKLKMIEEETSLTV 362

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
             ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363 QSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483 REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 542

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543 TATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 622 RKLR 625
           RKLR
Sbjct: 603 RKLR 606


>gi|342903626|ref|ZP_08725435.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21621]
 gi|341954977|gb|EGT81443.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21621]
          Length = 627

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 309/636 (48%), Positives = 417/636 (65%), Gaps = 35/636 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 996  -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
               + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180  IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236  QQLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291  MKRVRYEERQLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351  ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531  SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 302/623 (48%), Positives = 408/623 (65%), Gaps = 35/623 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 206 -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
              + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180 IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236 QQLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291 MKRVRYEERQLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351 ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531 SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 591 GKQFDVTRERIRQIEAKALRKLR 613


>gi|260775520|ref|ZP_05884417.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
            BAA-450]
 gi|260608701|gb|EEX34866.1| RNA polymerase sigma factor RpoD [Vibrio coralliilyticus ATCC
            BAA-450]
          Length = 617

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 311/614 (50%), Positives = 416/614 (67%), Gaps = 12/614 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-------- 996
            KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +           
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 997  -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKE 1054
              + + + +  + + +      S D   E+   +  E +L KF+ +   F   + A  + 
Sbjct: 183  IGSELAESDLEDEDAEEEDAEESEDDEEEEDTGIDPELALEKFTALRNTFQNYQLACNEY 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    MP
Sbjct: 243  GNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + ++
Sbjct: 303  KKSFITLFTGNESSEAWLDEILSSDKPYAEKIRRSEDDIRRSIMKLKVIEEETSLTVQNI 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483  LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATST 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 603  RHPSRSETLRSFLD 616



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 304/601 (50%), Positives = 407/601 (67%), Gaps = 12/601 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-------- 206
           KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +           
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 207 -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKE 264
             + + + +  + + +      S D   E+   +  E +L KF+ +   F   + A  + 
Sbjct: 183 IGSELAESDLEDEDAEEEDAEESEDDEEEEDTGIDPELALEKFTALRNTFQNYQLACNEY 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    MP
Sbjct: 243 GNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + ++
Sbjct: 303 KKSFITLFTGNESSEAWLDEILSSDKPYAEKIRRSEDDIRRSIMKLKVIEEETSLTVQNI 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A + 
Sbjct: 483 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATST 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|285019606|ref|YP_003377317.1| RNA polymerase sigma-70 factor, rpod protein [Xanthomonas albilineans
            GPE PC73]
 gi|283474824|emb|CBA17323.1| probable rna polymerase sigma-70 factor, rpod protein [Xanthomonas
            albilineans GPE PC73]
          Length = 620

 Score =  562 bits (1449), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 302/607 (49%), Positives = 402/607 (66%), Gaps = 11/607 (1%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G  D        V+    ++
Sbjct: 132  EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPVVVAEDDS 191

Query: 1008 NEEKILIESSSADLSTEQLEKL------KYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                   +           E          E   +   +S  + K +KA+ K G   +  
Sbjct: 192  AAADAAGDEDEDADVDASEEDAGPTGPDPAEVARRMEVLSAEYAKFKKAYAKNGAEHKLV 251

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             K  N+I+   + ++      + L   LR+ + QV + E+++L +  +   MPR  FI+ 
Sbjct: 252  AKLRNDIAEVFVTLKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRS 311

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M
Sbjct: 312  WEGNQTNVVWVDDALKRKQKWSSALRDVKDQIIAEQEATVGVEQSTYLSLTELKEISRAM 371

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372  AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 432  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 491

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+
Sbjct: 492  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVR 551

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 552  DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 611

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 612  QLRSFLD 618



 Score =  546 bits (1408), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 295/594 (49%), Positives = 392/594 (65%), Gaps = 11/594 (1%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G  D        V+    ++
Sbjct: 132 EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPVVVAEDDS 191

Query: 218 NEEKILIESSSADLSTEQLEKL------KYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                  +           E          E   +   +S  + K +KA+ K G   +  
Sbjct: 192 AAADAAGDEDEDADVDASEEDAGPTGPDPAEVARRMEVLSAEYAKFKKAYAKNGAEHKLV 251

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            K  N+I+   + ++      + L   LR+ + QV + E+++L +  +   MPR  FI+ 
Sbjct: 252 AKLRNDIAEVFVTLKLPLPLTDALVRKLRDAMAQVKEHERRVLHLATHVARMPRKDFIRS 311

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M
Sbjct: 312 WEGNQTNVVWVDDALKRKQKWSSALRDVKDQIIAEQEATVGVEQSTYLSLTELKEISRAM 371

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372 AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 432 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 491

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+
Sbjct: 492 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVR 551

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|169794936|ref|YP_001712729.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii AYE]
 gi|184159289|ref|YP_001847628.1| DNA-directed RNA polymerase, sigma subunit [Acinetobacter baumannii
            ACICU]
 gi|213157659|ref|YP_002320457.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii AB0057]
 gi|215482482|ref|YP_002324668.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB307-0294]
 gi|239502295|ref|ZP_04661605.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB900]
 gi|260557301|ref|ZP_05829517.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
            19606 = CIP 70.34]
 gi|301346958|ref|ZP_07227699.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB056]
 gi|301513036|ref|ZP_07238273.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB058]
 gi|301596278|ref|ZP_07241286.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB059]
 gi|332854224|ref|ZP_08435244.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332866334|ref|ZP_08436939.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332872549|ref|ZP_08440518.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
 gi|384132980|ref|YP_005515592.1| rpoD [Acinetobacter baumannii 1656-2]
 gi|384144394|ref|YP_005527104.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii
            MDR-ZJ06]
 gi|385238728|ref|YP_005800067.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter baumannii TCDC-AB0715]
 gi|387122791|ref|YP_006288673.1| sigma-70 family RNA polymerase sigma factor [Acinetobacter baumannii
            MDR-TJ]
 gi|403673953|ref|ZP_10936230.1| rpoD [Acinetobacter sp. NCTC 10304]
 gi|407933873|ref|YP_006849516.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii TYTH-1]
 gi|416149389|ref|ZP_11602867.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter baumannii AB210]
 gi|417546113|ref|ZP_12197199.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC032]
 gi|417554525|ref|ZP_12205594.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-81]
 gi|417561268|ref|ZP_12212147.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC137]
 gi|417564186|ref|ZP_12215060.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC143]
 gi|417569946|ref|ZP_12220804.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC189]
 gi|417574515|ref|ZP_12225369.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Canada
            BC-5]
 gi|417576047|ref|ZP_12226892.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-17]
 gi|417868750|ref|ZP_12513755.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH1]
 gi|417874554|ref|ZP_12519404.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH2]
 gi|417876559|ref|ZP_12521322.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH3]
 gi|417884161|ref|ZP_12528368.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH4]
 gi|421202871|ref|ZP_15660016.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii AC12]
 gi|421536045|ref|ZP_15982297.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii AC30]
 gi|421624458|ref|ZP_16065329.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC098]
 gi|421629637|ref|ZP_16070363.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC180]
 gi|421633819|ref|ZP_16074446.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-13]
 gi|421647238|ref|ZP_16087657.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-251]
 gi|421652290|ref|ZP_16092650.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC0162]
 gi|421656222|ref|ZP_16096532.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-72]
 gi|421657445|ref|ZP_16097711.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-83]
 gi|421667823|ref|ZP_16107876.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC087]
 gi|421672623|ref|ZP_16112578.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC099]
 gi|421676693|ref|ZP_16116597.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC065]
 gi|421678240|ref|ZP_16118125.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC111]
 gi|421687421|ref|ZP_16127147.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-143]
 gi|421694702|ref|ZP_16134321.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-692]
 gi|421699879|ref|ZP_16139400.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-58]
 gi|421704548|ref|ZP_16143992.1| rpoD [Acinetobacter baumannii ZWS1122]
 gi|421708325|ref|ZP_16147703.1| rpoD [Acinetobacter baumannii ZWS1219]
 gi|421789747|ref|ZP_16225994.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-82]
 gi|421795632|ref|ZP_16231712.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-21]
 gi|421799404|ref|ZP_16235396.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Canada BC1]
 gi|421806365|ref|ZP_16242234.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-A-694]
 gi|421809986|ref|ZP_16245816.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC035]
 gi|424051168|ref|ZP_17788702.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab11111]
 gi|424058864|ref|ZP_17796357.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab33333]
 gi|424062328|ref|ZP_17799815.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab44444]
 gi|425750708|ref|ZP_18868664.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-348]
 gi|425755250|ref|ZP_18873071.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-113]
 gi|445403969|ref|ZP_21430804.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-57]
 gi|445464409|ref|ZP_21449612.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC338]
 gi|169147863|emb|CAM85726.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
            during exponential growth [Acinetobacter baumannii AYE]
 gi|183210883|gb|ACC58281.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter baumannii ACICU]
 gi|193078173|gb|ABO13119.2| sigma D (sigma 70) factor of RNA polymerase major sigma factor during
            exponential growth [Acinetobacter baumannii ATCC 17978]
 gi|213056819|gb|ACJ41721.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii AB0057]
 gi|213988184|gb|ACJ58483.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            AB307-0294]
 gi|260409407|gb|EEX02709.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii ATCC
            19606 = CIP 70.34]
 gi|322509200|gb|ADX04654.1| rpoD [Acinetobacter baumannii 1656-2]
 gi|323519229|gb|ADX93610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter baumannii TCDC-AB0715]
 gi|332728149|gb|EGJ59537.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013150]
 gi|332734682|gb|EGJ65786.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6013113]
 gi|332739235|gb|EGJ70093.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii 6014059]
 gi|333364481|gb|EGK46495.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
            [Acinetobacter baumannii AB210]
 gi|342228575|gb|EGT93458.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH2]
 gi|342232217|gb|EGT96998.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH1]
 gi|342234683|gb|EGT99323.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH4]
 gi|342237429|gb|EGU01899.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter baumannii
            ABNIH3]
 gi|347594887|gb|AEP07608.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii
            MDR-ZJ06]
 gi|385877283|gb|AFI94378.1| RNA polymerase sigma factor, sigma-70 family [Acinetobacter baumannii
            MDR-TJ]
 gi|395523850|gb|EJG11939.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC137]
 gi|395554169|gb|EJG20175.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC189]
 gi|395555942|gb|EJG21943.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC143]
 gi|395569268|gb|EJG29930.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-17]
 gi|398327592|gb|EJN43725.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii AC12]
 gi|400210083|gb|EJO41053.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Canada
            BC-5]
 gi|400384001|gb|EJP42679.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC032]
 gi|400390942|gb|EJP57989.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-81]
 gi|404565267|gb|EKA70436.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-143]
 gi|404567346|gb|EKA72468.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-692]
 gi|404571154|gb|EKA76218.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-58]
 gi|404664802|gb|EKB32779.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab33333]
 gi|404666279|gb|EKB34230.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab11111]
 gi|404672371|gb|EKB40204.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Ab44444]
 gi|407189843|gb|EKE61065.1| rpoD [Acinetobacter baumannii ZWS1122]
 gi|407190381|gb|EKE61599.1| rpoD [Acinetobacter baumannii ZWS1219]
 gi|407902454|gb|AFU39285.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii TYTH-1]
 gi|408505836|gb|EKK07553.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC0162]
 gi|408506170|gb|EKK07885.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-72]
 gi|408516674|gb|EKK18245.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-251]
 gi|408700759|gb|EKL46206.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC180]
 gi|408701373|gb|EKL46803.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC098]
 gi|408705805|gb|EKL51135.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-13]
 gi|408713396|gb|EKL58566.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-83]
 gi|409986018|gb|EKO42219.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter baumannii AC30]
 gi|410378693|gb|EKP31304.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC099]
 gi|410378815|gb|EKP31425.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC065]
 gi|410382012|gb|EKP34568.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC087]
 gi|410392427|gb|EKP44788.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC111]
 gi|410397663|gb|EKP49907.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-82]
 gi|410401305|gb|EKP53453.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-21]
 gi|410406862|gb|EKP58860.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-A-694]
 gi|410409642|gb|EKP61567.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Canada BC1]
 gi|410413777|gb|EKP65592.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC035]
 gi|425485393|gb|EKU51786.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-348]
 gi|425494918|gb|EKU61109.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-113]
 gi|444779685|gb|ELX03662.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC338]
 gi|444782565|gb|ELX06463.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-57]
 gi|452950516|gb|EME55973.1| RNA polymerase sigma factor sigma-70 [Acinetobacter baumannii
            MSP4-16]
          Length = 628

 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/613 (47%), Positives = 412/613 (67%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEDVEELEEEDE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
               K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194  SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++++
Sbjct: 314  QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  546 bits (1406), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 285/600 (47%), Positives = 403/600 (67%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEDVEELEEEDE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
              K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 194 SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++++
Sbjct: 314 QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|254509368|ref|ZP_05121455.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
 gi|219547710|gb|EED24748.1| RNA polymerase sigma factor [Vibrio parahaemolyticus 16]
          Length = 620

 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 313/617 (50%), Positives = 415/617 (67%), Gaps = 15/617 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L      +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-------------SLIKFSNISFHFDKMRKAF 1051
              +   +  +E   A+ + E+ E+ + E             +L KF+ +   F   + A 
Sbjct: 183  IGSELAESDLEDEDAEDADEEDEESEDEESEEEDTGIDPEFALEKFTALRNTFQNYQLAC 242

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
             + G  S     AH  + +     R T K  + L D LR  + +V   E+ I++  V   
Sbjct: 243  NEYGSESPKATVAHEMVIDVFKEFRLTPKQFDYLVDELRTSMERVRTQERLIMKASVEYG 302

Query: 1112 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 1171
             MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +
Sbjct: 303  KMPKKSFIALFSGNESSDAWLDEILASDKPYADKIRRSEDDIRRSIAKLKIIEEETSLTV 362

Query: 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 1231
             +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363  QNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 1232 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291
            VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423  VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351
             EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483  REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 542

Query: 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411
               S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543  TAGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 1412 RKLRHPSRYYKLKIFLE 1428
            RKLRHPSR   L+ FL+
Sbjct: 603  RKLRHPSRSETLRSFLD 619



 Score =  547 bits (1410), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 306/604 (50%), Positives = 406/604 (67%), Gaps = 15/604 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L      +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDETITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-------------SLIKFSNISFHFDKMRKAF 261
             +   +  +E   A+ + E+ E+ + E             +L KF+ +   F   + A 
Sbjct: 183 IGSELAESDLEDEDAEDADEEDEESEDEESEEEDTGIDPEFALEKFTALRNTFQNYQLAC 242

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
            + G  S     AH  + +     R T K  + L D LR  + +V   E+ I++  V   
Sbjct: 243 NEYGSESPKATVAHEMVIDVFKEFRLTPKQFDYLVDELRTSMERVRTQERLIMKASVEYG 302

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPL 381
            MP+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L +
Sbjct: 303 KMPKKSFIALFSGNESSDAWLDEILASDKPYADKIRRSEDDIRRSIAKLKIIEEETSLTV 362

Query: 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441
            +++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKA
Sbjct: 363 QNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 422

Query: 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 501
           VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G
Sbjct: 423 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMG 482

Query: 502 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561
            EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A
Sbjct: 483 REPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 542

Query: 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621
              S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKAL
Sbjct: 543 TAGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 602

Query: 622 RKLR 625
           RKLR
Sbjct: 603 RKLR 606


>gi|419838508|ref|ZP_14361933.1| RNA polymerase sigma factor RpoD [Haemophilus haemolyticus HK386]
 gi|386910273|gb|EIJ74930.1| RNA polymerase sigma factor RpoD [Haemophilus haemolyticus HK386]
          Length = 627

 Score =  562 bits (1448), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 309/636 (48%), Positives = 417/636 (65%), Gaps = 35/636 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 996  -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
               + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180  IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236  QQLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291  MKRVRYEERQLQKILVDISGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351  ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531  SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  547 bits (1409), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 302/623 (48%), Positives = 408/623 (65%), Gaps = 35/623 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 206 -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
              + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180 IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236 QQLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291 MKRVRYEERQLQKILVDISGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351 ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531 SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 591 GKQFDVTRERIRQIEAKALRKLR 613


>gi|319788464|ref|YP_004147939.1| RNA polymerase sigma-70 subunit RpoD [Pseudoxanthomonas suwonensis
            11-1]
 gi|317466976|gb|ADV28708.1| RNA polymerase, sigma 70 subunit, RpoD [Pseudoxanthomonas suwonensis
            11-1]
          Length = 618

 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 310/607 (51%), Positives = 407/607 (67%), Gaps = 10/607 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  SNITS-----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            ++  +     DD   E   AAL+ +DS+ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREIDDTAAEEAAAALTALDSEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRV--I 1001
            IEEGL  +  A+ S P ++  +L   +     + ++ E+V G   L+D+       V   
Sbjct: 130  IEEGLGQVQAALGSVPASVEALLEEYELHKAGKKRLAEVVVGFNDLLDETPEPPAPVEDT 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
                   E++    +   +           E   +   ++    K +KA  K G   +  
Sbjct: 190  ADADAEGEDEEEDVAEDDEAEAGPTGPDPAEVARRMEQLAADLAKFKKAHAKAGAQDKKV 249

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            IK    ++ + +  +      + L   LR+ + ++   E+++L +  N   MPR  FI+ 
Sbjct: 250  IKLRAEMAEQFVTFKLPLPLTDVLVRKLRDVLTEIKDRERRVLHLATNVARMPRKDFIRA 309

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N++NL WVD   K +  ++  L      I   QQ  I ++  + L L+D+R+I R++
Sbjct: 310  WEGNQVNLEWVDEVLKRKQKWSSALRDVKDQIIAEQQATIAIEQAMCLDLSDIREIGRQL 369

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370  AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 430  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 489

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D+  N ++   V+
Sbjct: 490  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDSTTNTNLMETVR 549

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 550  DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 609

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 610  QLRSFLD 616



 Score =  546 bits (1406), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 303/594 (51%), Positives = 397/594 (66%), Gaps = 10/594 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 SNITS-----DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           ++  +     DD   E   AAL+ +DS+ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREIDDTAAEEAAAALTALDSEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRV--I 211
           IEEGL  +  A+ S P ++  +L   +     + ++ E+V G   L+D+       V   
Sbjct: 130 IEEGLGQVQAALGSVPASVEALLEEYELHKAGKKRLAEVVVGFNDLLDETPEPPAPVEDT 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
                  E++    +   +           E   +   ++    K +KA  K G   +  
Sbjct: 190 ADADAEGEDEEEDVAEDDEAEAGPTGPDPAEVARRMEQLAADLAKFKKAHAKAGAQDKKV 249

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           IK    ++ + +  +      + L   LR+ + ++   E+++L +  N   MPR  FI+ 
Sbjct: 250 IKLRAEMAEQFVTFKLPLPLTDVLVRKLRDVLTEIKDRERRVLHLATNVARMPRKDFIRA 309

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N++NL WVD   K +  ++  L      I   QQ  I ++  + L L+D+R+I R++
Sbjct: 310 WEGNQVNLEWVDEVLKRKQKWSSALRDVKDQIIAEQQATIAIEQAMCLDLSDIREIGRQL 369

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 370 AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 429

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 430 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 489

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D+  N ++   V+
Sbjct: 490 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDSTTNTNLMETVR 549

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|113461378|ref|YP_719447.1| RNA polymerase sigma factor RpoD [Haemophilus somnus 129PT]
 gi|112823421|gb|ABI25510.1| RNA polymerase, sigma 70 subunit, RpoD [Haemophilus somnus 129PT]
          Length = 595

 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 298/604 (49%), Positives = 416/604 (68%), Gaps = 36/604 (5%)

Query: 851  INDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITSDDDVEEATEAALS 909
            +ND LPED++D + IE +I+    M I V E V D + LML+ NIT +D VEEAT+  LS
Sbjct: 1    MNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADDLMLNENITDEDAVEEATQV-LS 59

Query: 910  TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 969
            +V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG+ ++  A+++ P  +  +L
Sbjct: 60   SVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAVAAYPKALNYLL 119

Query: 970  IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN---KNNNEEKI-------------- 1012
                 + +  +++ +++ G +D N      +I+ +     ++EE +              
Sbjct: 120  EQYTLVEEGGMRLADLITGFVDPNAVVEEEIIETDDILTEDDEEHVESNVDVNDEEEEED 179

Query: 1013 -----LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN---SESYIKA 1064
                  ++S S +    ++ + K+E+L           K   A EK G +   ++ +I+A
Sbjct: 180  SEDNSNVDSDSDNTIAPEVAREKFEAL------RIQHQKTLAAIEKYGRSRKQAKDHIQA 233

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
              +I  +    R   K  + L + +R+ +  V Q E+QI ++VV+   MP+ +F K+F  
Sbjct: 234  LADIFTQ---FRLVPKQFDALVNYMRDMMKSVRQHERQIQKLVVDLAKMPKENFQKLFIG 290

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
            NE +  W+D     +  ++  L ++  ++++   +L+ ++ +  L ++ +R+I  K+  G
Sbjct: 291  NESSEGWLDKLLLARKPWSERLIQHESAVRQSINQLLKIEQETNLTISQIREICDKVAQG 350

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 351  ELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 410

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E     +A +M 
Sbjct: 411  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQKMGREATSEELAERMG 470

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   S+R+   ++L
Sbjct: 471  MPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLRAATHEVL 530

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+
Sbjct: 531  EGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLR 590

Query: 1425 IFLE 1428
             FL+
Sbjct: 591  SFLD 594



 Score =  546 bits (1408), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 291/591 (49%), Positives = 407/591 (68%), Gaps = 36/591 (6%)

Query: 61  INDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NITSDDDVEEATEAALS 119
           +ND LPED++D + IE +I+    M I V E V D + LML+ NIT +D VEEAT+  LS
Sbjct: 1   MNDHLPEDLVDADQIEDVIQMINDMGIQVLESVPDADDLMLNENITDEDAVEEATQV-LS 59

Query: 120 TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEIL 179
           +V+++ GRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG+ ++  A+++ P  +  +L
Sbjct: 60  SVEAELGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAVAAYPKALNYLL 119

Query: 180 IAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN---KNNNEEKI-------------- 222
                + +  +++ +++ G +D N      +I+ +     ++EE +              
Sbjct: 120 EQYTLVEEGGMRLADLITGFVDPNAVVEEEIIETDDILTEDDEEHVESNVDVNDEEEEED 179

Query: 223 -----LIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN---SESYIKA 274
                 ++S S +    ++ + K+E+L           K   A EK G +   ++ +I+A
Sbjct: 180 SEDNSNVDSDSDNTIAPEVAREKFEAL------RIQHQKTLAAIEKYGRSRKQAKDHIQA 233

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
             +I  +    R   K  + L + +R+ +  V Q E+QI ++VV+   MP+ +F K+F  
Sbjct: 234 LADIFTQ---FRLVPKQFDALVNYMRDMMKSVRQHERQIQKLVVDLAKMPKENFQKLFIG 290

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
           NE +  W+D     +  ++  L ++  ++++   +L+ ++ +  L ++ +R+I  K+  G
Sbjct: 291 NESSEGWLDKLLLARKPWSERLIQHESAVRQSINQLLKIEQETNLTISQIREICDKVAQG 350

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 351 ELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 410

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E     +A +M 
Sbjct: 411 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQKMGREATSEELAERMG 470

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   S+R+   ++L
Sbjct: 471 MPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDNTLELPLDSATAQSLRAATHEVL 530

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 531 EGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 581


>gi|226951573|ref|ZP_03822037.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter sp. ATCC 27244]
 gi|406035630|ref|ZP_11042994.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter parvus DSM
            16617 = CIP 108168]
 gi|226837676|gb|EEH70059.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter sp. ATCC 27244]
          Length = 626

 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 299/611 (48%), Positives = 410/611 (67%), Gaps = 18/611 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN----------NRVIKG 1003
            ++H+I+  P  +  +L   +     E ++ +I+ G +D                    K 
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEDEAEIEEEKS 193

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNS 1058
              +  +E  L +    +  ++   +         + I+F+ +   ++  +   EK G NS
Sbjct: 194  PTSTTKEVKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAIIEKHGRNS 253

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +    A   ++   +  +FT +  + + + +R   +Q+   E++I+   V +  M R  F
Sbjct: 254  KEAEAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTF 313

Query: 1119 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
               FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + D++DI
Sbjct: 314  RTTFPEQESNPAWLDEQIAKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDI 373

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 374  SKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 433

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P 
Sbjct: 434  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPE 493

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  ++
Sbjct: 494  ELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLK 553

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 554  EATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 613

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FLE
Sbjct: 614  SRSEHLRSFLE 624



 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 291/598 (48%), Positives = 401/598 (67%), Gaps = 18/598 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN----------NRVIKG 213
           ++H+I+  P  +  +L   +     E ++ +I+ G +D                    K 
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEDEAEIEEEKS 193

Query: 214 NKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGYNS 268
             +  +E  L +    +  ++   +         + I+F+ +   ++  +   EK G NS
Sbjct: 194 PTSTTKEVKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAIIEKHGRNS 253

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +    A   ++   +  +FT +  + + + +R   +Q+   E++I+   V +  M R  F
Sbjct: 254 KEAEAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTF 313

Query: 329 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
              FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + D++DI
Sbjct: 314 RTTFPEQESNPAWLDEQIAKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDI 373

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 374 SKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 433

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P 
Sbjct: 434 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPE 493

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  ++
Sbjct: 494 ELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLK 553

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 EATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611


>gi|417550833|ref|ZP_12201912.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-18]
 gi|421199047|ref|ZP_15656212.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC109]
 gi|421455377|ref|ZP_15904721.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-123]
 gi|421623243|ref|ZP_16064131.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC074]
 gi|421642158|ref|ZP_16082684.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-235]
 gi|421662800|ref|ZP_16102956.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC110]
 gi|421690740|ref|ZP_16130407.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-116]
 gi|421792741|ref|ZP_16228889.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-2]
 gi|445441977|ref|ZP_21442229.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-A-92]
 gi|445460074|ref|ZP_21447983.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC047]
 gi|445479905|ref|ZP_21455282.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-78]
 gi|445490672|ref|ZP_21459333.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii AA-014]
 gi|395565943|gb|EJG27590.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC109]
 gi|400211615|gb|EJO42577.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-123]
 gi|400386658|gb|EJP49732.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-18]
 gi|404563820|gb|EKA69016.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-116]
 gi|408513710|gb|EKK15324.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii IS-235]
 gi|408693551|gb|EKL39152.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC074]
 gi|408714316|gb|EKL59467.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC110]
 gi|410399380|gb|EKP51574.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-2]
 gi|444764287|gb|ELW88608.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-A-92]
 gi|444765440|gb|ELW89735.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii AA-014]
 gi|444772493|gb|ELW96609.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii Naval-78]
 gi|444773309|gb|ELW97405.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii OIFC047]
          Length = 625

 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 293/613 (47%), Positives = 412/613 (67%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 11   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 70

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 131  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEDVEELEEEDE 190

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
               K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 191  SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 250

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 251  NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 310

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++++
Sbjct: 311  QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIK 370

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 371  DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 430

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 431  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 490

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 491  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 550

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 611  HPSRSEHLRSFLE 623



 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 285/600 (47%), Positives = 403/600 (67%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 11  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 70

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 131 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEDVEELEEEDE 190

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
              K+  E K+  +    +   +   +         + ++F+ +   + + +   EK G 
Sbjct: 191 SSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFAELEAAWAQTKAVIEKHGR 250

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A  +++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 251 NSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 310

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L +++++
Sbjct: 311 QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELGLNVSEIK 370

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 371 DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 430

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 431 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 490

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 491 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 550

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 551 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|402758142|ref|ZP_10860398.1| rpoD [Acinetobacter sp. NCTC 7422]
          Length = 627

 Score =  561 bits (1446), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 301/612 (49%), Positives = 412/612 (67%), Gaps = 19/612 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L   +     E ++ +I+ G +D     +   +   +   EE+  
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEEAEIEEEDS 193

Query: 1014 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 1057
              S   D+  +  ++ +                  + ++FS +   +++ +    K G N
Sbjct: 194  SSSKGKDVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFSELEAAWNETKSVVAKHGRN 253

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            SE    A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R  
Sbjct: 254  SEEAKAALEALAAVFMMFKFTPRLFDIISEMIRGTHEQIRSNEREIMRYAVRRGRMDRNQ 313

Query: 1118 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ D+ L + D++D
Sbjct: 314  FRTTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 373

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374  ISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  +
Sbjct: 494  EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGL 553

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 554  KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 613

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FLE
Sbjct: 614  PSRSEHLRSFLE 625



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 293/599 (48%), Positives = 403/599 (67%), Gaps = 19/599 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L   +     E ++ +I+ G +D     +   +   +   EE+  
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEEAEIEEEDS 193

Query: 224 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 267
             S   D+  +  ++ +                  + ++FS +   +++ +    K G N
Sbjct: 194 SSSKGKDVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFSELEAAWNETKSVVAKHGRN 253

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           SE    A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R  
Sbjct: 254 SEEAKAALEALAAVFMMFKFTPRLFDIISEMIRGTHEQIRSNEREIMRYAVRRGRMDRNQ 313

Query: 328 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           F   FPE E N  W+D +  K   +    L +  P +   QQK+ +++ D+ L + D++D
Sbjct: 314 FRTTFPEQESNPAWLDEQIAKAPAETKAHLEKVRPDVLAFQQKIADIEKDLGLNVKDIKD 373

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374 ISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  +
Sbjct: 494 EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGL 553

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 612


>gi|294651232|ref|ZP_06728560.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
            19194]
 gi|292822885|gb|EFF81760.1| RNA polymerase sigma factor RpoD [Acinetobacter haemolyticus ATCC
            19194]
          Length = 626

 Score =  561 bits (1446), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 300/611 (49%), Positives = 416/611 (68%), Gaps = 18/611 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L   +     E ++ +I+ G +D         +  ++   EE+  
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEDEAEIEEEES 193

Query: 1014 IESSSADLSTEQLEKLKYE---------------SLIKFSNISFHFDKMRKAFEKEGYNS 1058
              S++ ++  +  ++ + E               + I+F+ +   ++  +   EK G NS
Sbjct: 194  PTSTTKEVKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAIIEKHGRNS 253

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +    A   ++   +  +FT +  + + + +R   +Q+   E++I+   V +  M R  F
Sbjct: 254  KEAEAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTF 313

Query: 1119 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
               FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + D++DI
Sbjct: 314  RTTFPEQESNPAWLDEQIAKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDI 373

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 374  SKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 433

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P 
Sbjct: 434  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPE 493

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  ++
Sbjct: 494  ELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLK 553

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
               +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 554  EATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 613

Query: 1418 SRYYKLKIFLE 1428
            SR   L+ FLE
Sbjct: 614  SRSEHLRSFLE 624



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 292/598 (48%), Positives = 407/598 (68%), Gaps = 18/598 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L   +     E ++ +I+ G +D         +  ++   EE+  
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEEIPEVLEDEAEIEEEES 193

Query: 224 IESSSADLSTEQLEKLKYE---------------SLIKFSNISFHFDKMRKAFEKEGYNS 268
             S++ ++  +  ++ + E               + I+F+ +   ++  +   EK G NS
Sbjct: 194 PTSTTKEVKLDDDDEEESESDDDSEGDSGPDPEVAKIRFTELETAWNDTKAIIEKHGRNS 253

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +    A   ++   +  +FT +  + + + +R   +Q+   E++I+   V +  M R  F
Sbjct: 254 KEAEAALEALAAVFMMFKFTPRLFDIISEMIRGTHDQIRANEREIMRYAVRRGRMDRTTF 313

Query: 329 IKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
              FPE E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + D++DI
Sbjct: 314 RTTFPEQESNPAWLDEQIAKAPAEIKTHLEKVRPDVLAFQQKIADIEKELGLNVKDIKDI 373

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 374 SKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 433

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P 
Sbjct: 434 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTPE 493

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  ++
Sbjct: 494 ELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGLK 553

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 EATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611


>gi|299768976|ref|YP_003731002.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter oleivorans
            DR1]
 gi|298699064|gb|ADI89629.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter oleivorans
            DR1]
          Length = 627

 Score =  561 bits (1446), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 299/616 (48%), Positives = 415/616 (67%), Gaps = 27/616 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
             T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DTADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------------------- 994
            ++++I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEDDA 193

Query: 995  -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 1053
             ++  + +K + +  +E+   +  S   S    E  K    I+F+ +   + K +   EK
Sbjct: 194  PATPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAK----IRFNELESAWTKTKGIIEK 249

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M
Sbjct: 250  HGRNSPEADEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRM 309

Query: 1114 PRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 1172
             R  F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + 
Sbjct: 310  DRTQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVA 369

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 370  EIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 429

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G 
Sbjct: 430  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGR 489

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA 
Sbjct: 490  EPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAAT 549

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
            +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 550  SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 609

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR   L+ FLE
Sbjct: 610  KLRHPSRSEHLRSFLE 625



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 291/603 (48%), Positives = 406/603 (67%), Gaps = 27/603 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
            T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DTADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF------------------- 204
           ++++I+  P  +  +L   +     E ++ +I+ G +D                      
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEDDA 193

Query: 205 -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
            ++  + +K + +  +E+   +  S   S    E  K    I+F+ +   + K +   EK
Sbjct: 194 PATPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAK----IRFNELESAWTKTKGIIEK 249

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M
Sbjct: 250 HGRNSPEADEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRM 309

Query: 324 PRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLN 382
            R  F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + 
Sbjct: 310 DRTQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVA 369

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV
Sbjct: 370 EIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 429

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G 
Sbjct: 430 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGR 489

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA 
Sbjct: 490 EPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAAT 549

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
           +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALR
Sbjct: 550 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 609

Query: 623 KLR 625
           KLR
Sbjct: 610 KLR 612


>gi|262401783|ref|ZP_06078349.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
 gi|262352200|gb|EEZ01330.1| RNA polymerase sigma factor RpoD [Vibrio sp. RC586]
          Length = 627

 Score =  561 bits (1446), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 319/631 (50%), Positives = 417/631 (66%), Gaps = 36/631 (5%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3    QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  +  AI+  P TI  IL   D++   E+++ +    LI      N+   +  
Sbjct: 123  KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTD----LIAGFVDPNDMETEAP 178

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------------KF 1037
               +   I  E + ADL+ E  E    E                              KF
Sbjct: 179  TATH---IGSELTEADLADEDDEIAAEEDEDEDEDGEGNSESSDSEEEVGIDPELAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + +   F  ++ A  + G +S    +A   + +     R T K  + L +TLR  +++V 
Sbjct: 236  NELRGKFQNLQLAVNEFGRDSNQASEASGLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 295

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
              E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   
Sbjct: 296  TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVREQEEDIRRSI 355

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 356  QKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 415

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 416  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 475

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 476  KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 535

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 536  FIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 595

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 596  VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 626



 Score =  546 bits (1408), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 312/618 (50%), Positives = 408/618 (66%), Gaps = 36/618 (5%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E   D 
Sbjct: 3   QNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDA 62

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           + L LS+ T+  D+D  EA  AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  +  AI+  P TI  IL   D++   E+++ +    LI      N+   +  
Sbjct: 123 KRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTD----LIAGFVDPNDMETEAP 178

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLI---------------------------KF 247
              +   I  E + ADL+ E  E    E                              KF
Sbjct: 179 TATH---IGSELTEADLADEDDEIAAEEDEDEDEDGEGNSESSDSEEEVGIDPELAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           + +   F  ++ A  + G +S    +A   + +     R T K  + L +TLR  +++V 
Sbjct: 236 NELRGKFQNLQLAVNEFGRDSNQASEASGLVLDIFREFRLTPKQFDHLVETLRTSMDRVR 295

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
             E+ +++ VV    MP+  FI +F  NE N  W+D        Y   +      I+   
Sbjct: 296 TQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVQKVREQEEDIRRSI 355

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 356 QKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQF 415

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 416 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 475

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGD
Sbjct: 476 KLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD 535

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 536 FIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 595

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 596 VTRERIRQIEAKALRKLR 613


>gi|293610908|ref|ZP_06693207.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|427423825|ref|ZP_18913966.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-136]
 gi|292826560|gb|EFF84926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|425699485|gb|EKU69100.1| RNA polymerase sigma factor RpoD [Acinetobacter baumannii WC-136]
          Length = 628

 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 294/613 (47%), Positives = 411/613 (67%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
              +K+  E K+  +    +   +   +         + ++F+ +   + K +   EK G 
Sbjct: 194  SSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFTELEAAWAKTKAVVEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  NSPEAEEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314  QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  545 bits (1403), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 286/600 (47%), Positives = 402/600 (67%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
             +K+  E K+  +    +   +   +         + ++F+ +   + K +   EK G 
Sbjct: 194 SSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFTELEAAWAKTKAVVEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 NSPEAEEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP+ E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +++
Sbjct: 314 QFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKELSLSVAEIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|307246390|ref|ZP_07528466.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 1 str. 4074]
 gi|307255376|ref|ZP_07537186.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 9 str. CVJ13261]
 gi|307259826|ref|ZP_07541544.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 11 str. 56153]
 gi|306852723|gb|EFM84952.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 1 str. 4074]
 gi|306861685|gb|EFM93669.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 9 str. CVJ13261]
 gi|306866124|gb|EFM97994.1| RNA polymerase sigma factor rpoD [Actinobacillus pleuropneumoniae
            serovar 11 str. 56153]
          Length = 619

 Score =  561 bits (1445), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/623 (48%), Positives = 407/623 (65%), Gaps = 50/623 (8%)

Query: 837  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 895
            I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15   IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 896  SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 955
             +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75   DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 956  HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 1002
             A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134  CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 1003 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 1048
                          GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194  VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 1049 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 1105
            +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239  QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 1106 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 1165
              V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296  YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQ 355

Query: 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 1225
               L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356  TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 1226 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 1285
            IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416  IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 1286 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 1345
             LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476  CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405
             P D+A   S+R    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536  LPLDSATAESLRLATNEVLEGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 1406 IEAKALRKLRHPSRYYKLKIFLE 1428
            IEAKALRKLRHPSR   L+ FL+
Sbjct: 596  IEAKALRKLRHPSRSETLRSFLD 618



 Score =  546 bits (1406), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 298/610 (48%), Positives = 398/610 (65%), Gaps = 50/610 (8%)

Query: 47  IKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS-NIT 105
           I  G+E+GYLT SE++D LPE+++D E IE II+    M I V E   DT+ LML+ NI 
Sbjct: 15  IAQGREQGYLTISEVHDHLPEELVDAEQIEDIIQMINDMGIKVLETAPDTDELMLAENIA 74

Query: 106 SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMI 165
            +D VEEAT+  LSTV+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+ ++ 
Sbjct: 75  DEDVVEEATKV-LSTVESELGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINEVQ 133

Query: 166 HAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK------------- 212
            A++  P  + E++    ++ +  +++ ++V   +D N  ++  +               
Sbjct: 134 CAVAEYPEALTELIGFYAQVEEGTMRLSDLVTAFVDPNIQADEALEDLDVDLDDEEEAED 193

Query: 213 --------------GNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR 258
                         GN +  ++     S   +L+ E           KF  +    +K  
Sbjct: 194 VADVDDESEEEESDGNADTGDDN----SIDPELARE-----------KFYALREQHEKAL 238

Query: 259 KAFEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILE 315
           +A +K G +   S   I+A ++I  E    R   K  + L ++++  + QV   E+QI  
Sbjct: 239 QAIQKHGRSHKKSREQIQALSDIFRE---FRLVPKQFDLLVESMQKMMKQVRSEERQIQR 295

Query: 316 IVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQT 375
             V    M +  F+K+F  NE +  W++     +      L   I  I+     L  ++ 
Sbjct: 296 YAVEYAQMKKADFLKLFQGNETSEEWIEKAINAKKGAAPKLANYIDQIRVNIDNLQRMEQ 355

Query: 376 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGN 435
              L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGN
Sbjct: 356 TTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 415

Query: 436 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQ 495
           IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ
Sbjct: 416 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQ 475

Query: 496 ILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENML 555
            LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFI+DE++ 
Sbjct: 476 CLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIQDESLE 535

Query: 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615
            P D+A   S+R    ++L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQ
Sbjct: 536 LPLDSATAESLRLATNEVLEGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 616 IEAKALRKLR 625
           IEAKALRKLR
Sbjct: 596 IEAKALRKLR 605


>gi|417839650|ref|ZP_12485823.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M19107]
 gi|341952016|gb|EGT78559.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M19107]
          Length = 627

 Score =  560 bits (1444), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 308/636 (48%), Positives = 417/636 (65%), Gaps = 35/636 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 996  -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
               + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180  IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236  QQLKEQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291  MKRVRYEERQLQKILVDIAGMPKDDFEKLIMTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L +++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351  ILEALSNLASIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531  SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 301/623 (48%), Positives = 408/623 (65%), Gaps = 35/623 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 206 -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
              + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180 IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236 QQLKEQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 291 MKRVRYEERQLQKILVDIAGMPKDDFEKLIMTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L +++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351 ILEALSNLASIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531 SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 591 GKQFDVTRERIRQIEAKALRKLR 613


>gi|343498224|ref|ZP_08736263.1| RNA polymerase sigma factor RpoD [Vibrio tubiashii ATCC 19109]
 gi|418477566|ref|ZP_13046694.1| RNA polymerase sigma factor RpoD [Vibrio tubiashii NCIMB 1337 = ATCC
            19106]
 gi|342824665|gb|EGU59200.1| RNA polymerase sigma factor RpoD [Vibrio tubiashii ATCC 19109]
 gi|384574831|gb|EIF05290.1| RNA polymerase sigma factor RpoD [Vibrio tubiashii NCIMB 1337 = ATCC
            19106]
          Length = 618

 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 310/615 (50%), Positives = 413/615 (67%), Gaps = 13/615 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + ++++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123  KRIEDGINQVQNSVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 1053
              +   +  +E   A+   E+  +   E           +L KF+ +   F   + A  +
Sbjct: 183  IGSELAESDLEDEDAEEKDEEESEDDEEEEEDTGIDPELALEKFTALRNTFQNYQLACNE 242

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243  YGNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKM 302

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + +
Sbjct: 303  PKKSFITLFTGNESSEAWLDEILSSDKPYAEKIRRSEDDIRRSIAKLKVIEEETSLTVQN 362

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363  IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483  PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543  GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 603  LRHPSRSETLRSFLD 617



 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 303/602 (50%), Positives = 404/602 (67%), Gaps = 13/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + ++++  P TI  IL   DK+   E+++ +++ G +D +          +
Sbjct: 123 KRIEDGINQVQNSVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 263
             +   +  +E   A+   E+  +   E           +L KF+ +   F   + A  +
Sbjct: 183 IGSELAESDLEDEDAEEKDEEESEDDEEEEEDTGIDPELALEKFTALRNTFQNYQLACNE 242

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243 YGNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKM 302

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + +
Sbjct: 303 PKKSFITLFTGNESSEAWLDEILSSDKPYAEKIRRSEDDIRRSIAKLKVIEEETSLTVQN 362

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543 GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 624 LR 625
           LR
Sbjct: 603 LR 604


>gi|417841159|ref|ZP_12487264.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M19501]
 gi|341949753|gb|EGT76354.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M19501]
          Length = 627

 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 308/636 (48%), Positives = 417/636 (65%), Gaps = 35/636 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 996  -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
               + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180  IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236  QQLKEQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  G+P+  F K+   N  N  WV    K    +   L +    
Sbjct: 291  MKRVRYEERQLQKILVDIAGIPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351  ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531  SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 301/623 (48%), Positives = 408/623 (65%), Gaps = 35/623 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 206 -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
              + VI  N + + E    ES SAD+   + E                         KF
Sbjct: 180 IEEHNVIDENFSEDGE----ESESADVEDNEDEDESESESTSDSSESDNSIDPEVAREKF 235

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 236 QQLKEQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 290

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  G+P+  F K+   N  N  WV    K    +   L +    
Sbjct: 291 MKRVRYEERQLQKILVDIAGIPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEER 350

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351 ILEALNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531 SHLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 591 GKQFDVTRERIRQIEAKALRKLR 613


>gi|262281266|ref|ZP_06059048.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
            RUH2202]
 gi|262257497|gb|EEY76233.1| RNA polymerase sigma factor rpoD [Acinetobacter calcoaceticus
            RUH2202]
          Length = 627

 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 295/612 (48%), Positives = 413/612 (67%), Gaps = 19/612 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
             T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DTTDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +   +   +   EE+  
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEEEA 193

Query: 1014 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 1057
                + ++  +  E+ +                  + ++F+ +   + K +   EK G N
Sbjct: 194  PAVPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAKVRFNELEAAWTKTKAIIEKHGRN 253

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S     A   ++   +  +FT +  + + + +R    Q+   E++++   V +  M R  
Sbjct: 254  SPEADDALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREVMRYAVRRGRMDRTQ 313

Query: 1118 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            F   FP+ E N  W+D +  K   +    L +  P I   QQK+ +++ ++ L + +++D
Sbjct: 314  FRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDILAFQQKIADIEKELNLSVAEIKD 373

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374  ISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  +
Sbjct: 494  EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGL 553

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 554  KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 613

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FLE
Sbjct: 614  PSRSEHLRSFLE 625



 Score =  544 bits (1401), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 287/599 (47%), Positives = 404/599 (67%), Gaps = 19/599 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
            T+D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DTTDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +   +   +   EE+  
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEETELEEEEA 193

Query: 224 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 267
               + ++  +  E+ +                  + ++F+ +   + K +   EK G N
Sbjct: 194 PAVPAKEVKLDDDEEDEESESDDDSEGESGPDPEVAKVRFNELEAAWTKTKAIIEKHGRN 253

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S     A   ++   +  +FT +  + + + +R    Q+   E++++   V +  M R  
Sbjct: 254 SPEADDALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREVMRYAVRRGRMDRTQ 313

Query: 328 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           F   FP+ E N  W+D +  K   +    L +  P I   QQK+ +++ ++ L + +++D
Sbjct: 314 FRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDILAFQQKIADIEKELNLSVAEIKD 373

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374 ISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA +  +
Sbjct: 494 EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPIDAATSEGL 553

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 612


>gi|406040078|ref|ZP_11047433.1| rpoD [Acinetobacter ursingii DSM 16037 = CIP 107286]
          Length = 628

 Score =  560 bits (1443), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 295/613 (48%), Positives = 410/613 (66%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFGEST 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++H+I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEEAELEEDEE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
              +K   E K+  +    +   +   + +       + ++F  +   ++  +   E+ G 
Sbjct: 194  SSSKTTKEVKLDDDDEEEESEGDDDSEGESGPDPEVAKVRFEELEAAWNNTKAVIEQHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +SE   +A  ++++  +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  SSEQANEALESLASVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP  E N  W D +  K   +    L +  P +   QQK+ +++ D+ L + +++
Sbjct: 314  QFRTSFPGQESNPAWFDEQIAKAPAEMRSYLEKVRPDVLAFQQKIADIEKDLDLHVREIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  DISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  544 bits (1401), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 287/600 (47%), Positives = 401/600 (66%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFGEST 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+S+ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVESEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++H+I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLHSIAYWPNAVEVVLQEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEEAELEEDEE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
             +K   E K+  +    +   +   + +       + ++F  +   ++  +   E+ G 
Sbjct: 194 SSSKTTKEVKLDDDDEEEESEGDDDSEGESGPDPEVAKVRFEELEAAWNNTKAVIEQHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +SE   +A  ++++  +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 SSEQANEALESLASVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRN 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP  E N  W D +  K   +    L +  P +   QQK+ +++ D+ L + +++
Sbjct: 314 QFRTSFPGQESNPAWFDEQIAKAPAEMRSYLEKVRPDVLAFQQKIADIEKDLDLHVREIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 DISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|261250212|ref|ZP_05942788.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891 = ATCC
            33934]
 gi|417953296|ref|ZP_12596343.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891 = ATCC
            33934]
 gi|260939328|gb|EEX95314.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891 = ATCC
            33934]
 gi|342817471|gb|EGU52352.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891 = ATCC
            33934]
          Length = 618

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 311/615 (50%), Positives = 411/615 (66%), Gaps = 13/615 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 1053
              +   +  +E   A+   E  +    E           +L KF+ +   F   + A  +
Sbjct: 183  IGSELAESELEDEDAEEKEESDDSDDEEEEEDTGIDPELALEKFTALRNTFQNYQLACNE 242

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243  YGNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKATVEYGKM 302

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            P+  FI +F  NE    W+D        Y   + R+   I+    KL  ++ +  L + +
Sbjct: 303  PKKSFITLFTGNESTDAWLDEILASDKPYAEKVRRSEDDIRRSISKLKIIEEETSLTVQN 362

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363  IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483  PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543  GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FL+
Sbjct: 603  LRHPSRSETLRSFLD 617



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 304/602 (50%), Positives = 402/602 (66%), Gaps = 13/602 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE+G+  + +A++  P TI  IL   D+I   E+++ +++ G +D +          +
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDRIQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYE-----------SLIKFSNISFHFDKMRKAFEK 263
             +   +  +E   A+   E  +    E           +L KF+ +   F   + A  +
Sbjct: 183 IGSELAESELEDEDAEEKEESDDSDDEEEEEDTGIDPELALEKFTALRNTFQNYQLACNE 242

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    M
Sbjct: 243 YGNESPKATLAHEMVIDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKATVEYGKM 302

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           P+  FI +F  NE    W+D        Y   + R+   I+    KL  ++ +  L + +
Sbjct: 303 PKKSFITLFTGNESTDAWLDEILASDKPYAEKVRRSEDDIRRSISKLKIIEEETSLTVQN 362

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 363 IKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 422

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E
Sbjct: 423 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 482

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A  
Sbjct: 483 PLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATA 542

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 543 GSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 602

Query: 624 LR 625
           LR
Sbjct: 603 LR 604


>gi|50085952|ref|YP_047462.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter sp. ADP1]
 gi|49531928|emb|CAG69640.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
            during exponential growth [Acinetobacter sp. ADP1]
          Length = 629

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/618 (48%), Positives = 411/618 (66%), Gaps = 29/618 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  + T
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGDST 73

Query: 896  SDDDVEEATEAA-LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
              D+V E   AA L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D+
Sbjct: 74   EADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRDV 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            +H+I+  P  +  +L   +     E ++ +I+ G +D     +   I        E    
Sbjct: 134  LHSIAYWPNAVEVVLQEYNDYVTGERRLADILSGYLDPETDDD---IPEVLEEEAELEED 190

Query: 1015 ESSSADLSTEQLEKLKYE-----------------------SLIKFSNISFHFDKMRKAF 1051
            + S++  +T+ + KL  +                       + ++F  +   +   +   
Sbjct: 191  DESTSKTTTKDV-KLDDDDEEEEESEGDDDSEGDSGPDPEIAKVRFEELEAAWKNTKTVI 249

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            EK G NSE    A  +++   +  +FT +  + + + +R     +   E++++   V + 
Sbjct: 250  EKHGRNSEEANAALESLATVFMMFKFTPRLFDIISEMIRGTHENIRSNEREVMRYAVRRG 309

Query: 1112 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             M R  F   FP  E N  W++ +  K  ++    L +  P I+  QQK+  ++ D+ L 
Sbjct: 310  RMDRTQFRTSFPGQESNPAWLEEQIAKAPNESKAYLEKVRPDIQAFQQKIAEIEQDLNLN 369

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + ++++I ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 370  VREIKEIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 429

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 430  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 489

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 490  GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDA 549

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 550  ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 609

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FLE
Sbjct: 610  LRKLRHPSRSEHLRSFLE 627



 Score =  543 bits (1400), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 289/605 (47%), Positives = 402/605 (66%), Gaps = 29/605 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  + T
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGDST 73

Query: 106 SDDDVEEATEAA-LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
             D+V E   AA L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D+
Sbjct: 74  EADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRDV 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           +H+I+  P  +  +L   +     E ++ +I+ G +D     +   I        E    
Sbjct: 134 LHSIAYWPNAVEVVLQEYNDYVTGERRLADILSGYLDPETDDD---IPEVLEEEAELEED 190

Query: 225 ESSSADLSTEQLEKLKYE-----------------------SLIKFSNISFHFDKMRKAF 261
           + S++  +T+ + KL  +                       + ++F  +   +   +   
Sbjct: 191 DESTSKTTTKDV-KLDDDDEEEEESEGDDDSEGDSGPDPEIAKVRFEELEAAWKNTKTVI 249

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           EK G NSE    A  +++   +  +FT +  + + + +R     +   E++++   V + 
Sbjct: 250 EKHGRNSEEANAALESLATVFMMFKFTPRLFDIISEMIRGTHENIRSNEREVMRYAVRRG 309

Query: 322 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            M R  F   FP  E N  W++ +  K  ++    L +  P I+  QQK+  ++ D+ L 
Sbjct: 310 RMDRTQFRTSFPGQESNPAWLEEQIAKAPNESKAYLEKVRPDIQAFQQKIAEIEQDLNLN 369

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + ++++I ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 370 VREIKEIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 429

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 430 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 489

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 490 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDA 549

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 550 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 609

Query: 621 LRKLR 625
           LRKLR
Sbjct: 610 LRKLR 614


>gi|417844281|ref|ZP_12490326.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21639]
 gi|341956912|gb|EGT83327.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21639]
          Length = 618

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 307/627 (48%), Positives = 415/627 (66%), Gaps = 26/627 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 996  -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDK 1046
               + VI  + + + EK    S SAD+   + E                KF  +     K
Sbjct: 180  IEEHNVIDESFSEDGEK----SESADVENNEDEDESESDNSIDPEVAREKFQQLKDQHTK 235

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIEK 1101
                 EK G + +   +A N I+   LG      R   K  + L  +++  + +V   E+
Sbjct: 236  TLTVIEKHGRSGK---RAQNQIAQ--LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYEER 290

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 1161
            Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L 
Sbjct: 291  QLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEERILEALSNLA 350

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
             ++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 351  GIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 410

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 411  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 470

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            ISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SM++P+GDD+DSHLGDFIED
Sbjct: 471  ISRQLLQEMGREAIPEELAERMGMPEDKIRKVLKIAKEPISMDAPIGDDDDSHLGDFIED 530

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
              +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 531  STLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 590

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  RIRQIEAKALRKLRHPSRSETLRSFLD 617



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 300/614 (48%), Positives = 406/614 (66%), Gaps = 26/614 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 206 -SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDK 256
              + VI  + + + EK    S SAD+   + E                KF  +     K
Sbjct: 180 IEEHNVIDESFSEDGEK----SESADVENNEDEDESESDNSIDPEVAREKFQQLKDQHTK 235

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIEK 311
                EK G + +   +A N I+   LG      R   K  + L  +++  + +V   E+
Sbjct: 236 TLTVIEKHGRSGK---RAQNQIAQ--LGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYEER 290

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLI 371
           Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L 
Sbjct: 291 QLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEERILEALSNLA 350

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
            ++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 351 GIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 410

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R
Sbjct: 411 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNR 470

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           ISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SM++P+GDD+DSHLGDFIED
Sbjct: 471 ISRQLLQEMGREAIPEELAERMGMPEDKIRKVLKIAKEPISMDAPIGDDDDSHLGDFIED 530

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
             +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRE
Sbjct: 531 STLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 590

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 591 RIRQIEAKALRKLR 604


>gi|323493625|ref|ZP_08098746.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
 gi|323312148|gb|EGA65291.1| RNA polymerase sigma factor RpoD [Vibrio brasiliensis LMG 20546]
          Length = 617

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 311/614 (50%), Positives = 414/614 (67%), Gaps = 12/614 (1%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 884
            +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3    QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 885  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63   DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-------- 996
            KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +           
Sbjct: 123  KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 997  -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKE 1054
              + + +    + + +   E S      E+   +  E +L KF+ +   F   + A  + 
Sbjct: 183  IGSELAESELEDEDAEDEEEDSDDSEEEEEDTGIDPELALEKFTALRNTFQNFQLACNEY 242

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    MP
Sbjct: 243  GNESPKAQIAHELVLDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMP 302

Query: 1115 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
            +  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + ++
Sbjct: 303  KKSFITLFTGNESSDAWLDEILASDKPYAEKIRRSEDDIRRSIAKLKVIEEETSLTVQNI 362

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363  KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   
Sbjct: 483  LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAT 542

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
            S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543  SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FL+
Sbjct: 603  RHPSRSETLRSFLD 616



 Score =  545 bits (1404), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 304/601 (50%), Positives = 405/601 (67%), Gaps = 12/601 (1%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV--L 94
           +N + + K L+  GKE+GYLT++E+ND LP +I+D E +E II+    M I V E     
Sbjct: 3   QNPQSQLKQLVIKGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIRVVETAPDA 62

Query: 95  DTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           D   L   +  +D+D  EA  AALS+V+++ GRT DP++MYMREMG+VELLTR+GEI+IA
Sbjct: 63  DDLALNDDDTITDEDAAEAAAAALSSVENEIGRTTDPVRMYMREMGTVELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-------- 206
           KRIE+G+  + +A++  P TI  IL   DK+   E+++ +++ G +D +           
Sbjct: 123 KRIEDGINQVQNAVAEYPGTIPYILEQFDKVQAEELRLTDLITGFVDPDADETAAPTATH 182

Query: 207 -NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-SLIKFSNISFHFDKMRKAFEKE 264
             + + +    + + +   E S      E+   +  E +L KF+ +   F   + A  + 
Sbjct: 183 IGSELAESELEDEDAEDEEEDSDDSEEEEEDTGIDPELALEKFTALRNTFQNFQLACNEY 242

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G  S     AH  + +     R T K  + L + LR  + +V   E+ I++  V    MP
Sbjct: 243 GNESPKAQIAHELVLDVFKEFRLTPKQFDYLVEELRTSMERVRTQERLIMKASVEYGKMP 302

Query: 325 RLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
           +  FI +F  NE +  W+D        Y   + R+   I+    KL  ++ +  L + ++
Sbjct: 303 KKSFITLFTGNESSDAWLDEILASDKPYAEKIRRSEDDIRRSIAKLKVIEEETSLTVQNI 362

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DI+R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 363 KDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 422

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP
Sbjct: 423 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 482

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +A +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   
Sbjct: 483 LPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATAT 542

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
           S++   KD+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 543 SLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 602

Query: 625 R 625
           R
Sbjct: 603 R 603


>gi|146281106|ref|YP_001171259.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
 gi|145569311|gb|ABP78417.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri A1501]
          Length = 569

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 290/564 (51%), Positives = 392/564 (69%), Gaps = 10/564 (1%)

Query: 875  MDISVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            M I+V E   D + L+L+   +D+   E   AAL+ V++D GRT DP++MYMREMG+VEL
Sbjct: 5    MGINVFETAPDADALLLAEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVEL 64

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN- 993
            LTR+GEIEIAKRIEEG+++++ AI+  P T+  IL   ++++    ++ +I+ G ID + 
Sbjct: 65   LTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDD 124

Query: 994  -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHF 1044
              ++  + ++        K +++    D   E   + +          + ++F  ++   
Sbjct: 125  DGAAAPQEVEPETPQTTAKPVVDDKDDDDEEESDTEEEEGDGGPDPEVARVRFGAVAEQL 184

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +K  KA +K G  S+   +    ++   + I+   K  + L + +R+ +NQ+   E+ I+
Sbjct: 185  EKANKALKKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIM 244

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
            ++ V    MPR  F++ FP NE NL+W +     +  Y   +      I+  QQKLI L+
Sbjct: 245  QLCVRDARMPRADFLRQFPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELE 304

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
                L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 305  QQCELAIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 364

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 365  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 424

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+LQE G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M
Sbjct: 425  QMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAM 484

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
             +P D A   S++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 485  QSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 544

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKLRHP+R   L+ FL+
Sbjct: 545  QIEAKALRKLRHPTRSEHLRSFLD 568



 Score =  546 bits (1406), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 284/551 (51%), Positives = 383/551 (69%), Gaps = 10/551 (1%)

Query: 85  MDISVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 144
           M I+V E   D + L+L+   +D+   E   AAL+ V++D GRT DP++MYMREMG+VEL
Sbjct: 5   MGINVFETAPDADALLLAEADTDEAAAEEAAAALAAVETDIGRTTDPVRMYMREMGTVEL 64

Query: 145 LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN- 203
           LTR+GEIEIAKRIEEG+++++ AI+  P T+  IL   ++++    ++ +I+ G ID + 
Sbjct: 65  LTREGEIEIAKRIEEGIREVMSAIAHFPGTVDSILADYERVTNEGGRLSDILSGYIDPDD 124

Query: 204 -FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE--------SLIKFSNISFHF 254
             ++  + ++        K +++    D   E   + +          + ++F  ++   
Sbjct: 125 DGAAAPQEVEPETPQTTAKPVVDDKDDDDEEESDTEEEEGDGGPDPEVARVRFGAVAEQL 184

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +K  KA +K G  S+   +    ++   + I+   K  + L + +R+ +NQ+   E+ I+
Sbjct: 185 EKANKALKKHGRASQQATEELEALAILFMPIKLVPKQYDALVERVRDALNQIRAQERAIM 244

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
           ++ V    MPR  F++ FP NE NL+W +     +  Y   +      I+  QQKLI L+
Sbjct: 245 QLCVRDARMPRADFLRQFPSNETNLDWAEQLAAGKSKYAEAIGNRKEEIQRCQQKLIELE 304

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
               L + D++DINR+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 305 QQCELAIADIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 364

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR
Sbjct: 365 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISR 424

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+LQE G EP P  +  +MEMPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  M
Sbjct: 425 QMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSAM 484

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
            +P D A   S++   +++L+ LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIR
Sbjct: 485 QSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 544

Query: 615 QIEAKALRKLR 625
           QIEAKALRKLR
Sbjct: 545 QIEAKALRKLR 555


>gi|445420373|ref|ZP_21435491.1| RNA polymerase sigma factor RpoD [Acinetobacter sp. WC-743]
 gi|444758960|gb|ELW83448.1| RNA polymerase sigma factor RpoD [Acinetobacter sp. WC-743]
          Length = 627

 Score =  560 bits (1442), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 291/615 (47%), Positives = 411/615 (66%), Gaps = 22/615 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   ++
Sbjct: 11   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFDGNS 70

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
               D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71   EAGDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L         E ++ +I+ G +D         +  +++ + ++  
Sbjct: 131  VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEDESEDLDEDE 190

Query: 1014 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 1054
              SS+      +L+    +                   + ++F  +   ++  ++   + 
Sbjct: 191  TSSSTKPAKDVKLDDDDEDEESESDDDSEGESGPDPEIAKVRFDELEAVWNAAKETIAQH 250

Query: 1055 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 1114
            G NS   ++A   ++   +  +FT +  + + + +R    Q+   E++++   V +  M 
Sbjct: 251  GRNSAQGVEAMEALATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMD 310

Query: 1115 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
            R  F   FP  E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +
Sbjct: 311  RTQFRTSFPGQESNPAWLDEQIAKAPAEMKGYLEKVRPDVLAFQQKIADIEKELNLNVKE 370

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 371  IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 430

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 431  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 490

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
            P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +
Sbjct: 491  PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATS 550

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
              ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 551  EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 610

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR   L+ FLE
Sbjct: 611  LRHPSRSEHLRSFLE 625



 Score =  543 bits (1400), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 283/602 (47%), Positives = 402/602 (66%), Gaps = 22/602 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +T+  M   ++
Sbjct: 11  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPETDDAMFDGNS 70

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
              D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71  EAGDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L         E ++ +I+ G +D         +  +++ + ++  
Sbjct: 131 VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEDESEDLDEDE 190

Query: 224 IESSSADLSTEQLEKLKYE-------------------SLIKFSNISFHFDKMRKAFEKE 264
             SS+      +L+    +                   + ++F  +   ++  ++   + 
Sbjct: 191 TSSSTKPAKDVKLDDDDEDEESESDDDSEGESGPDPEIAKVRFDELEAVWNAAKETIAQH 250

Query: 265 GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMP 324
           G NS   ++A   ++   +  +FT +  + + + +R    Q+   E++++   V +  M 
Sbjct: 251 GRNSAQGVEAMEALATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMD 310

Query: 325 RLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
           R  F   FP  E N  W+D +  K   +    L +  P +   QQK+ +++ ++ L + +
Sbjct: 311 RTQFRTSFPGQESNPAWLDEQIAKAPAEMKGYLEKVRPDVLAFQQKIADIEKELNLNVKE 370

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           ++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVD
Sbjct: 371 IKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 430

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G E
Sbjct: 431 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGRE 490

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
           P P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +
Sbjct: 491 PTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATS 550

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRK
Sbjct: 551 EGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRK 610

Query: 624 LR 625
           LR
Sbjct: 611 LR 612


>gi|403051443|ref|ZP_10905927.1| rpoD [Acinetobacter bereziniae LMG 1003]
          Length = 630

 Score =  559 bits (1441), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 292/626 (46%), Positives = 415/626 (66%), Gaps = 22/626 (3%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            E+ +   +   LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   
Sbjct: 3    EMHSPTSQVAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAP 62

Query: 885  DTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +T+  M   ++   D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63   ETDDAMFDGNSEAGDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIS 122

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEG++D++H+I+  P  +  +L         E ++ +I+ G +D         + 
Sbjct: 123  IAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVL 182

Query: 1003 GNKNNNEEKILIESSSADLSTEQLEKLKYE-------------------SLIKFSNISFH 1043
             +++ + ++    SS+      +L+    +                   + ++F  +   
Sbjct: 183  EDESEDLDEDETSSSTKPAKDVKLDDDDEDEESESDDDSEGESGPDPEIAKVRFDELEAV 242

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
            ++  ++   + G NS   ++A   ++   +  +FT +  + + + +R    Q+   E+++
Sbjct: 243  WNAAKETIAQHGRNSAQGVEAMEALATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREV 302

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLIN 1162
            +   V +  M R  F   FP  E N  W+D +  K   +    L +  P +   QQK+ +
Sbjct: 303  MRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQIAKAPAEMKGYLEKVRPDVLAFQQKIAD 362

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            ++ ++ L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 363  IEKELNLNVKEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 422

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+
Sbjct: 423  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRV 482

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 483  SRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDS 542

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
            N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRER
Sbjct: 543  NITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRER 602

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLE 1428
            IRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 603  IRQIEAKALRKLRHPSRSEHLRSFLE 628



 Score =  543 bits (1399), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 284/613 (46%), Positives = 406/613 (66%), Gaps = 22/613 (3%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           E+ +   +   LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   
Sbjct: 3   EMHSPTSQVAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAP 62

Query: 95  DTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +T+  M   ++   D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63  ETDDAMFDGNSEAGDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIS 122

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEG++D++H+I+  P  +  +L         E ++ +I+ G +D         + 
Sbjct: 123 IAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVL 182

Query: 213 GNKNNNEEKILIESSSADLSTEQLEKLKYE-------------------SLIKFSNISFH 253
            +++ + ++    SS+      +L+    +                   + ++F  +   
Sbjct: 183 EDESEDLDEDETSSSTKPAKDVKLDDDDEDEESESDDDSEGESGPDPEIAKVRFDELEAV 242

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
           ++  ++   + G NS   ++A   ++   +  +FT +  + + + +R    Q+   E+++
Sbjct: 243 WNAAKETIAQHGRNSAQGVEAMEALATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREV 302

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLIN 372
           +   V +  M R  F   FP  E N  W+D +  K   +    L +  P +   QQK+ +
Sbjct: 303 MRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQIAKAPAEMKGYLEKVRPDVLAFQQKIAD 362

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
           ++ ++ L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 363 IEKELNLNVKEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 422

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+
Sbjct: 423 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRV 482

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 483 SRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDS 542

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
           N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRER
Sbjct: 543 NITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRER 602

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 603 IRQIEAKALRKLR 615


>gi|152978401|ref|YP_001344030.1| RNA polymerase sigma factor RpoD [Actinobacillus succinogenes 130Z]
 gi|150840124|gb|ABR74095.1| RNA polymerase, sigma 70 subunit, RpoD [Actinobacillus succinogenes
            130Z]
          Length = 623

 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 306/620 (49%), Positives = 403/620 (65%), Gaps = 20/620 (3%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+LI  GKE+GYLTF+E+ND LPED++D + IE II+    M I V E   D +
Sbjct: 4    NPQSQLKLLIAQGKEQGYLTFAEVNDHLPEDLVDTDQIEDIIQMINDMGIQVLETAPDAD 63

Query: 888  TLMLS-NITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
             L+L+ NIT  D+  VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELL R+GEI IA
Sbjct: 64   DLLLNENITDTDEDAVEEATQV-LSSVESELGRTTDPVRMYMREMGSVELLDREGEIGIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSN 997
            KRIE+G+ ++  AI+  P  I  +L    ++ +  I++ +++ G +D         FS +
Sbjct: 123  KRIEDGINEVQSAIAEYPEGITYLLDQYAQVEEGGIRLADLITGFVDPTVEESADEFSDD 182

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMRK 1049
                +      +  +  E+   + + +                   KF  +    DK   
Sbjct: 183  LADDEDADVEVDADLDDENEDEEDNNDNSSSSDDNDNSIDPEVAREKFYALRDQHDKTIA 242

Query: 1050 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 1109
               K G  S    +    +S      R   +  + L   +R  + ++   E+QI    V+
Sbjct: 243  TIAKHGRGSAKAREQMKALSEIFTQFRLVPRQFDVLVIPMRKMMKRIRAEERQIQRWAVD 302

Query: 1110 KCGMPRLHFIKVFPEN-EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 1168
               MP+  F+KVF    E N  W+      +  Y   L +   +I+    +L NL+ +  
Sbjct: 303  YARMPKDEFVKVFSTGKETNDAWLTKLLGGKKPYAEKLAKYADNIRASIARLQNLEQEAH 362

Query: 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 1228
            L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 363  LTIEQIRNIGDRISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 1229 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 1288
            MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQ
Sbjct: 423  MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQ 482

Query: 1289 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348
            E G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 483  EMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPL 542

Query: 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408
            D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 543  DSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 602

Query: 1409 KALRKLRHPSRYYKLKIFLE 1428
            KALRKLRHPSR   L+ FL+
Sbjct: 603  KALRKLRHPSRSETLRSFLD 622



 Score =  544 bits (1401), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 299/607 (49%), Positives = 394/607 (64%), Gaps = 20/607 (3%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+LI  GKE+GYLTF+E+ND LPED++D + IE II+    M I V E   D +
Sbjct: 4   NPQSQLKLLIAQGKEQGYLTFAEVNDHLPEDLVDTDQIEDIIQMINDMGIQVLETAPDAD 63

Query: 98  TLMLS-NITSDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
            L+L+ NIT  D+  VEEAT+  LS+V+S+ GRT DP++MYMREMGSVELL R+GEI IA
Sbjct: 64  DLLLNENITDTDEDAVEEATQV-LSSVESELGRTTDPVRMYMREMGSVELLDREGEIGIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-------FSSN 207
           KRIE+G+ ++  AI+  P  I  +L    ++ +  I++ +++ G +D         FS +
Sbjct: 123 KRIEDGINEVQSAIAEYPEGITYLLDQYAQVEEGGIRLADLITGFVDPTVEESADEFSDD 182

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMRK 259
               +      +  +  E+   + + +                   KF  +    DK   
Sbjct: 183 LADDEDADVEVDADLDDENEDEEDNNDNSSSSDDNDNSIDPEVAREKFYALRDQHDKTIA 242

Query: 260 AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVN 319
              K G  S    +    +S      R   +  + L   +R  + ++   E+QI    V+
Sbjct: 243 TIAKHGRGSAKAREQMKALSEIFTQFRLVPRQFDVLVIPMRKMMKRIRAEERQIQRWAVD 302

Query: 320 KCGMPRLHFIKVFPEN-EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIV 378
              MP+  F+KVF    E N  W+      +  Y   L +   +I+    +L NL+ +  
Sbjct: 303 YARMPKDEFVKVFSTGKETNDAWLTKLLGGKKPYAEKLAKYADNIRASIARLQNLEQEAH 362

Query: 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438
           L +  +R+I  ++  GE+KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGL
Sbjct: 363 LTIEQIRNIGDRISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498
           MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQ
Sbjct: 423 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQCLQ 482

Query: 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558
           E G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  +  P 
Sbjct: 483 EMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPL 542

Query: 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618
           D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEA
Sbjct: 543 DSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 602

Query: 619 KALRKLR 625
           KALRKLR
Sbjct: 603 KALRKLR 609


>gi|384426251|ref|YP_005635608.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv. raphani
            756C]
 gi|341935351|gb|AEL05490.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv. raphani
            756C]
          Length = 624

 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 308/611 (50%), Positives = 412/611 (67%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+ + P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E +  D   +  E+          E   +  N++  + K +KA+ K G  
Sbjct: 192  PVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYVKYGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             ++ +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKNVVKAREDMAAIFTTLKLPLPLTDSLVTQLREVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  543 bits (1399), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 301/598 (50%), Positives = 402/598 (67%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+ + P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E +  D   +  E+          E   +  N++  + K +KA+ K G  
Sbjct: 192 PVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYVKYGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            ++ +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKNVVKAREDMAAIFTTLKLPLPLTDSLVTQLREVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|21233164|ref|NP_639081.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            campestris str. ATCC 33913]
 gi|66770104|ref|YP_244866.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            campestris str. 8004]
 gi|32130006|sp|Q8P4H2.1|RPOD_XANCP RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|21115012|gb|AAM42993.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv. campestris
            str. ATCC 33913]
 gi|66575436|gb|AAY50846.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv. campestris
            str. 8004]
          Length = 624

 Score =  559 bits (1440), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 309/611 (50%), Positives = 411/611 (67%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+ + P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E +  D   +  E+          E   +  N++  + K +KA+ K G  
Sbjct: 192  PVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYVKYGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             ++  KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKNVAKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L +++DI
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  543 bits (1399), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 302/598 (50%), Positives = 401/598 (67%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+ + P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGTFPLSTELLLSDYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E +  D   +  E+          E   +  N++  + K +KA+ K G  
Sbjct: 192 PVAVDEDAVDEDADEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYVKYGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            ++  KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKNVAKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L +++DI
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLAEIKDI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|392552470|ref|ZP_10299607.1| RNA polymerase sigma factor [Pseudoalteromonas spongiae
            UST010723-006]
          Length = 614

 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 307/609 (50%), Positives = 411/609 (67%), Gaps = 13/609 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+LI+ GKE+GYLTF+E+ND LP+DIID E +E II     M I V E+  D + LM+
Sbjct: 8    QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSEQVEDIIGMINDMGIQVVENAPDADELMM 67

Query: 892  SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68   QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 1001
              +  +++  P  I  +L   D     ++++ +I+ G  D +            S     
Sbjct: 128  NQVQVSVAEYPEAINYLLEQWDNYLAEDVRLSDIISGFYDPDADETMISATHIGSELSEE 187

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            + +  +++ +   +    +  T    +   E+  K  N+   +++ R  FE++G +    
Sbjct: 188  ELDDEDSDLESDDDDDEEEADTGPCPEEAAENFEKLRNL---YNQARGIFEEKGRSHPDA 244

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +     I       +   K  +++   +R+ ++++   E+ I++ VV    MP+  F+K 
Sbjct: 245  VAIIAEIGEHFRTFKLMPKQFDRMVKNMRDMMDRIRVQERIIMKQVVQIAKMPKKTFVKN 304

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  NE +  W+D E      Y+  L      ++    KL  ++    L L  ++DINR+M
Sbjct: 305  FANNETDSAWLDREIASGELYSNKLAEVKFEVERCINKLRQMEESTGLNLERIKDINRRM 364

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 365  SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 424

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 425  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAE 484

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+++   
Sbjct: 485  RMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIESPVDSATMESLKNATH 544

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 545  DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSD 604

Query: 1422 KLKIFLEGK 1430
             LK FL+ K
Sbjct: 605  LLKSFLDFK 613



 Score =  543 bits (1400), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 301/602 (50%), Positives = 404/602 (67%), Gaps = 14/602 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+LI+ GKE+GYLTF+E+ND LP+DIID E +E II     M I V E+  D + LM+
Sbjct: 8   QLKLLIQKGKEQGYLTFAEVNDHLPQDIIDSEQVEDIIGMINDMGIQVVENAPDADELMM 67

Query: 102 SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              T+D+D  EA  AAL+TV+ + GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+
Sbjct: 68  QETTTDEDAAEAAAAALATVEKEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI 127

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------FSSNNRVI 211
             +  +++  P  I  +L   D     ++++ +I+ G  D +            S     
Sbjct: 128 NQVQVSVAEYPEAINYLLEQWDNYLAEDVRLSDIISGFYDPDADETMISATHIGSELSEE 187

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           + +  +++ +   +    +  T    +   E+  K  N+   +++ R  FE++G +    
Sbjct: 188 ELDDEDSDLESDDDDDEEEADTGPCPEEAAENFEKLRNL---YNQARGIFEEKGRSHPDA 244

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +     I       +   K  +++   +R+ ++++   E+ I++ VV    MP+  F+K 
Sbjct: 245 VAIIAEIGEHFRTFKLMPKQFDRMVKNMRDMMDRIRVQERIIMKQVVQIAKMPKKTFVKN 304

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  NE +  W+D E      Y+  L      ++    KL  ++    L L  ++DINR+M
Sbjct: 305 FANNETDSAWLDREIASGELYSNKLAEVKFEVERCINKLRQMEESTGLNLERIKDINRRM 364

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 365 SIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 424

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A 
Sbjct: 425 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPSPEELAE 484

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A   S+++   
Sbjct: 485 RMVMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSTIESPVDSATMESLKNATH 544

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHD 630
           D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D
Sbjct: 545 DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSD 604

Query: 631 WL 632
            L
Sbjct: 605 LL 606


>gi|381198266|ref|ZP_09905605.1| sigma D (sigma 70) factor of RNA polymerase, major sigma factor
            during exponential growth [Acinetobacter lwoffii WJ10621]
          Length = 627

 Score =  558 bits (1439), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 295/612 (48%), Positives = 409/612 (66%), Gaps = 19/612 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M    N
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEGGN 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L         E ++ +I+ G +D         +   ++  +E+  
Sbjct: 134  VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEEESEIDEEDS 193

Query: 1014 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 1057
               S+ D+  +  E+ +                  +  +F  ++  +   R   EK G +
Sbjct: 194  STKSTKDVKLDDDEEEEESESDDDSEGESGPDPEIAKARFDELTAAWKNTRTIIEKHGRS 253

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
            S+    A  +++   +  +FT +  + + + +R    Q+   E++++   V +  M R  
Sbjct: 254  SKEAEDALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMDRTQ 313

Query: 1118 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
            F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ D+ L +  +++
Sbjct: 314  FRTSFPGQESNFAWLDEQIAKASPDQKGYLEKVRPDVLAFQQKIADIEKDLGLDVKGIKE 373

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374  ISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  +
Sbjct: 494  EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGL 553

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 554  KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 613

Query: 1417 PSRYYKLKIFLE 1428
            PSR   L+ FLE
Sbjct: 614  PSRSEHLRSFLE 625



 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 287/599 (47%), Positives = 400/599 (66%), Gaps = 19/599 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M    N
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEGGN 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L         E ++ +I+ G +D         +   ++  +E+  
Sbjct: 134 VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEEESEIDEEDS 193

Query: 224 IESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGYN 267
              S+ D+  +  E+ +                  +  +F  ++  +   R   EK G +
Sbjct: 194 STKSTKDVKLDDDEEEEESESDDDSEGESGPDPEIAKARFDELTAAWKNTRTIIEKHGRS 253

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
           S+    A  +++   +  +FT +  + + + +R    Q+   E++++   V +  M R  
Sbjct: 254 SKEAEDALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMDRTQ 313

Query: 328 FIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
           F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ D+ L +  +++
Sbjct: 314 FRTSFPGQESNFAWLDEQIAKASPDQKGYLEKVRPDVLAFQQKIADIEKDLGLDVKGIKE 373

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 374 ISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 433

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP P
Sbjct: 434 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPTP 493

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  +
Sbjct: 494 EELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEGL 553

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 KEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 612


>gi|262369385|ref|ZP_06062713.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262315453|gb|EEY96492.1| DNA-directed RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 628

 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 297/613 (48%), Positives = 409/613 (66%), Gaps = 20/613 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M    N
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEGGN 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKGNKNNNEEKI 1012
            ++H+I+  P  +  +L         E ++ +I+ G +D         V++     +EE  
Sbjct: 134  VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEEESEIDEEDD 193

Query: 1013 LIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGY 1056
                S+ D+  +  E+ +                  +  +F  ++  +   R   EK G 
Sbjct: 194  SSTKSTKDVKLDDDEEEEESESDDDSEGESGPDPEIAKARFDELTAAWKNTRTIIEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            +S+    A  +++   +  +FT +  + + + +R    Q+   E++++   V +  M R 
Sbjct: 254  SSKEAEDALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 1175
             F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ D+ L +  ++
Sbjct: 314  QFRTSFPGQESNFAWLDEQIAKASPDQKGYLEKVRPDVLAFQQKIADIEKDLDLDVKGIK 373

Query: 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235
            +I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374  EISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 1295
            EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434  EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 1296 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494  PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554  LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613

Query: 1416 HPSRYYKLKIFLE 1428
            HPSR   L+ FLE
Sbjct: 614  HPSRSEHLRSFLE 626



 Score =  542 bits (1396), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 289/600 (48%), Positives = 400/600 (66%), Gaps = 20/600 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M    N
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEGGN 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIKGNKNNNEEKI 222
           ++H+I+  P  +  +L         E ++ +I+ G +D         V++     +EE  
Sbjct: 134 VLHSIAYWPNAVEVVLQEYKDYEAGERRLADILSGYLDPETDEAIPEVLEEESEIDEEDD 193

Query: 223 LIESSSADLSTEQLEKLKYE----------------SLIKFSNISFHFDKMRKAFEKEGY 266
               S+ D+  +  E+ +                  +  +F  ++  +   R   EK G 
Sbjct: 194 SSTKSTKDVKLDDDEEEEESESDDDSEGESGPDPEIAKARFDELTAAWKNTRTIIEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           +S+    A  +++   +  +FT +  + + + +R    Q+   E++++   V +  M R 
Sbjct: 254 SSKEAEDALESLATVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREVMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLR 385
            F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ D+ L +  ++
Sbjct: 314 QFRTSFPGQESNFAWLDEQIAKASPDQKGYLEKVRPDVLAFQQKIADIEKDLDLDVKGIK 373

Query: 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445
           +I+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKF
Sbjct: 374 EISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 433

Query: 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPD 505
           EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP 
Sbjct: 434 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREPT 493

Query: 506 PSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 565
           P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DAA +  
Sbjct: 494 PEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPVDAATSEG 553

Query: 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 554 LKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 613


>gi|78049468|ref|YP_365643.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            vesicatoria str. 85-10]
 gi|325926137|ref|ZP_08187498.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans 91-118]
 gi|346726561|ref|YP_004853230.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            citrumelo F1]
 gi|78037898|emb|CAJ25643.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
            vesicatoria str. 85-10]
 gi|325543482|gb|EGD14904.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas perforans 91-118]
 gi|346651308|gb|AEO43932.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            citrumelo F1]
          Length = 625

 Score =  558 bits (1438), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 305/612 (49%), Positives = 404/612 (66%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V      + ++    +  +A+           E   +  N++  + K +KA+ K G 
Sbjct: 192  PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 298/599 (49%), Positives = 394/599 (65%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V      + ++    +  +A+           E   +  N++  + K +KA+ K G 
Sbjct: 192 PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKAYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|325913856|ref|ZP_08176215.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria ATCC
            35937]
 gi|325539931|gb|EGD11568.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas vesicatoria ATCC
            35937]
          Length = 624

 Score =  558 bits (1437), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 308/611 (50%), Positives = 408/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +I+     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDIAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  542 bits (1396), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 301/598 (50%), Positives = 398/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +I+     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDIAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|58580221|ref|YP_199237.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae KACC
            10331]
 gi|58424815|gb|AAW73852.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae KACC
            10331]
          Length = 629

 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 299/611 (48%), Positives = 404/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 17   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 76

Query: 893  NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------KNFSSN 997
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D             ++ 
Sbjct: 137  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 196

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               +  +  + ++    + ++A+           E   +  N++  + K +K + K G  
Sbjct: 197  PVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVEVATRMQNLANEYAKFKKVYAKNGAE 256

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 257  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 316

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 317  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 376

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 377  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 436

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 437  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 496

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 497  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 556

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 557  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 616

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 617  SRSEQLRSFLD 627



 Score =  541 bits (1395), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 292/598 (48%), Positives = 394/598 (65%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 17  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 76

Query: 103 NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 77  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 136

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------KNFSSN 207
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D             ++ 
Sbjct: 137 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 196

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
              +  +  + ++    + ++A+           E   +  N++  + K +K + K G  
Sbjct: 197 PVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVEVATRMQNLANEYAKFKKVYAKNGAE 256

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 257 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 316

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 317 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 376

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 377 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 436

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 437 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 496

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 497 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 556

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 557 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 614


>gi|373467177|ref|ZP_09558478.1| RNA polymerase sigma factor RpoD [Haemophilus sp. oral taxon 851 str.
            F0397]
 gi|371759136|gb|EHO47882.1| RNA polymerase sigma factor RpoD [Haemophilus sp. oral taxon 851 str.
            F0397]
          Length = 627

 Score =  557 bits (1436), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 305/635 (48%), Positives = 419/635 (65%), Gaps = 33/635 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 993
            TR+ EI IAKRIEEG+ ++  +I++ P  + E+L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNELLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---------------KFS 1038
               +N + +    + EE    ES+  + + ++ E     +                 KF 
Sbjct: 180  IEEHNVIDESFSEDGEES---ESTDVEDNEDEDESEAESTSDSSESDNSIDPEVAREKFQ 236

Query: 1039 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQI 1093
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  +
Sbjct: 237  QLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMM 291

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
             +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I
Sbjct: 292  KRVRHEERQLQKILVDIAGMPKDDFEKLIITNGSNTEWVQKALKSSKPWAKRLPKYEERI 351

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
             E    L +++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+R
Sbjct: 352  LEALSNLASIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNR 411

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 412  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 471

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DS
Sbjct: 472  ETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 531

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVG
Sbjct: 532  HLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 591

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            KQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 592  KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 298/622 (47%), Positives = 410/622 (65%), Gaps = 33/622 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 203
           TR+ EI IAKRIEEG+ ++  +I++ P  + E+L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNELLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---------------KFS 248
              +N + +    + EE    ES+  + + ++ E     +                 KF 
Sbjct: 180 IEEHNVIDESFSEDGEES---ESTDVEDNEDEDESEAESTSDSSESDNSIDPEVAREKFQ 236

Query: 249 NISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQI 303
            +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  +
Sbjct: 237 QLKDQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMM 291

Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 363
            +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I
Sbjct: 292 KRVRHEERQLQKILVDIAGMPKDDFEKLIITNGSNTEWVQKALKSSKPWAKRLPKYEERI 351

Query: 364 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 423
            E    L +++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+R
Sbjct: 352 LEALSNLASIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNR 411

Query: 424 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483
           GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 412 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 471

Query: 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543
           ETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DS
Sbjct: 472 ETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 531

Query: 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 603
           HLGDFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVG
Sbjct: 532 HLGDFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 591

Query: 604 KQFDVTRERIRQIEAKALRKLR 625
           KQFDVTRERIRQIEAKALRKLR
Sbjct: 592 KQFDVTRERIRQIEAKALRKLR 613


>gi|417842428|ref|ZP_12488513.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21127]
 gi|341951640|gb|EGT78202.1| RNA polymerase sigma factor rpoD [Haemophilus haemolyticus M21127]
          Length = 627

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/632 (47%), Positives = 417/632 (65%), Gaps = 27/632 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG------- 988
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G       
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 989  -----LIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNIS 1041
                 +ID+NFS +   ++     + E      + +   + + +      +   KF  + 
Sbjct: 180  IEEHNVIDENFSEDGEELESADVEDNEDEDESEAESTSDSSESDNSIDPEVAREKFQQLK 239

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQV 1096
                K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V
Sbjct: 240  DQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRV 294

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
               E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E 
Sbjct: 295  RYEERQLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEERILEA 354

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
               L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 355  LNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQ 414

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 415  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 474

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLG
Sbjct: 475  NKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLG 534

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 535  DFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 594

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  DVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 296/619 (47%), Positives = 408/619 (65%), Gaps = 27/619 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG------- 198
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G       
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLADLITGFVDPNAE 179

Query: 199 -----LIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--KFSNIS 251
                +ID+NFS +   ++     + E      + +   + + +      +   KF  + 
Sbjct: 180 IEEHNVIDENFSEDGEELESADVEDNEDEDESEAESTSDSSESDNSIDPEVAREKFQQLK 239

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQV 306
               K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V
Sbjct: 240 DQHTKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRV 294

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
              E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E 
Sbjct: 295 RYEERQLQKILVDIAGMPKDDFEKLITTNGSNTEWVQKALKSSKPWAKRLPKYEERILEA 354

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
              L N++ +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 355 LNNLANIEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQ 414

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 415 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 474

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLG
Sbjct: 475 NKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLG 534

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED  +  P D+A   S+R    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQF
Sbjct: 535 DFIEDSTLELPLDSATAQSLRVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQF 594

Query: 607 DVTRERIRQIEAKALRKLR 625
           DVTRERIRQIEAKALRKLR
Sbjct: 595 DVTRERIRQIEAKALRKLR 613


>gi|289667862|ref|ZP_06488937.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            musacearum NCPPB 4381]
          Length = 624

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 408/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  541 bits (1394), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 398/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|289664793|ref|ZP_06486374.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            vasculorum NCPPB 702]
          Length = 624

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/611 (50%), Positives = 408/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D   E  E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  541 bits (1394), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 300/598 (50%), Positives = 398/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D   E  E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKSSYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|294625247|ref|ZP_06703887.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp. aurantifolii
            str. ICPB 11122]
 gi|292600475|gb|EFF44572.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp. aurantifolii
            str. ICPB 11122]
          Length = 621

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/610 (49%), Positives = 406/610 (66%), Gaps = 16/610 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------KNFSSNN 998
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D            ++  
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 999  RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 1058
             V   +    +E    +++  +      + +  E   +  N++  + K +K + K G   
Sbjct: 192  PVAVSDDEAVDEDDDDDAAEEEAGPTGPDPV--EVATRMENLANEYAKFKKVYAKNGAEH 249

Query: 1059 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 1118
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  F
Sbjct: 250  KLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDF 309

Query: 1119 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            I+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I+
Sbjct: 310  IRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEIS 369

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 370  RAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 429

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  
Sbjct: 430  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEE 489

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++  
Sbjct: 490  LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSE 549

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 550  TVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 609

Query: 1419 RYYKLKIFLE 1428
            R  +L+ FL+
Sbjct: 610  RSEQLRSFLD 619



 Score =  541 bits (1394), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/597 (49%), Positives = 396/597 (66%), Gaps = 16/597 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID---------KNFSSNN 208
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D            ++  
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 209 RVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNS 268
            V   +    +E    +++  +      + +  E   +  N++  + K +K + K G   
Sbjct: 192 PVAVSDDEAVDEDDDDDAAEEEAGPTGPDPV--EVATRMENLANEYAKFKKVYAKNGAEH 249

Query: 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHF 328
           +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  F
Sbjct: 250 KLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKDF 309

Query: 329 IKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           I+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I+
Sbjct: 310 IRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKEIS 369

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 370 RAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 429

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  
Sbjct: 430 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPEE 489

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++  
Sbjct: 490 LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLSE 549

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 TVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|84622216|ref|YP_449588.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae MAFF
            311018]
 gi|188574947|ref|YP_001911876.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
            PXO99A]
 gi|84366156|dbj|BAE67314.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae MAFF
            311018]
 gi|188519399|gb|ACD57344.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae PXO99A]
          Length = 624

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 302/611 (49%), Positives = 406/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------KNFSSN 997
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D             ++ 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 998  NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
               +  +  + ++    + ++A+           E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVEVATRMQNLANEYAKFKKVYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  541 bits (1394), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 295/598 (49%), Positives = 396/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID----------KNFSSN 207
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D             ++ 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 208 NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
              +  +  + ++    + ++A+           E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDALDEDDDEDGDDAAAEEEVGPTGPDPVEVATRMQNLANEYAKFKKVYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|194367344|ref|YP_002029954.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
            R551-3]
 gi|194350148|gb|ACF53271.1| RNA polymerase, sigma 70 subunit, RpoD [Stenotrophomonas maltophilia
            R551-3]
          Length = 618

 Score =  557 bits (1435), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 305/609 (50%), Positives = 403/609 (66%), Gaps = 14/609 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLAEEVAAPAAPAASD 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSE 1059
            + ++         D   +  ++          E   +   +S  F+  +KA  K   + +
Sbjct: 190  DGDDAGADADEEEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAVAK--GDKK 247

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            S +K    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI
Sbjct: 248  SLLKLREEMSAVFVTLKLPLPLTDVLTKQLRDTMAGIKSHERRVLNLATVTARMPRKDFI 307

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
            + +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L+DL++++R
Sbjct: 308  RSWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLDDLKELSR 367

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
             M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 368  AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 427

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +
Sbjct: 428  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEEL 487

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   
Sbjct: 488  AKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSET 547

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR
Sbjct: 548  VRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 607

Query: 1420 YYKLKIFLE 1428
              +L+ FL+
Sbjct: 608  SEQLRSFLD 616



 Score =  541 bits (1393), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 298/596 (50%), Positives = 393/596 (65%), Gaps = 14/596 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLAEEVAAPAAPAASD 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKY-------ESLIKFSNISFHFDKMRKAFEKEGYNSE 269
           + ++         D   +  ++          E   +   +S  F+  +KA  K   + +
Sbjct: 190 DGDDAGADADEEEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAVAK--GDKK 247

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           S +K    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI
Sbjct: 248 SLLKLREEMSAVFVTLKLPLPLTDVLTKQLRDTMAGIKSHERRVLNLATVTARMPRKDFI 307

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
           + +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L+DL++++R
Sbjct: 308 RSWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLDDLKELSR 367

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 368 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 427

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +
Sbjct: 428 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEEL 487

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   
Sbjct: 488 AKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSET 547

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 VRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|345429381|ref|YP_004822499.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus parainfluenzae
            T3T1]
 gi|301155442|emb|CBW14908.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus parainfluenzae
            T3T1]
          Length = 629

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 298/631 (47%), Positives = 421/631 (66%), Gaps = 23/631 (3%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1    MEQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDLIDPEYYDKLLQTLQHDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N +
Sbjct: 120  TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLDNYDQVEAGNYRLADLITGFVDPNIA 179

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KF 1037
            +   V+  ++N  +E++ +  ++AD+  E  E+ + +S                    +F
Sbjct: 180  AEE-VVNVDENFADEEVSV-GAAADVDDESDEEDESDSSSSSDDSDSDNSIDPEVARERF 237

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            S +     K      K G + +        +++     R   K  + L  +++N + +V 
Sbjct: 238  SALREQHTKTLATIAKHGRSGKRAKDQIAQLADIFKQFRLVPKQFDTLVLSMKNMMKRVR 297

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
              E+Q+ +++V+  GMP+  F  +   N  +  WV    K    +   L +    I+   
Sbjct: 298  AEERQLQKVLVDIAGMPKDEFEALIVANGSSDAWVAKALKSTKAWAKRLPKYEERIRLSL 357

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
              L N++    L +  +R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 358  DNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQF 417

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 418  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 477

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGD
Sbjct: 478  KLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGD 537

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 538  FIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 597

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 598  VTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  542 bits (1396), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 291/618 (47%), Positives = 412/618 (66%), Gaps = 23/618 (3%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1   MEQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDLIDPEYYDKLLQTLQHDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N +
Sbjct: 120 TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLDNYDQVEAGNYRLADLITGFVDPNIA 179

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI------------------KF 247
           +   V+  ++N  +E++ +  ++AD+  E  E+ + +S                    +F
Sbjct: 180 AEE-VVNVDENFADEEVSV-GAAADVDDESDEEDESDSSSSSDDSDSDNSIDPEVARERF 237

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           S +     K      K G + +        +++     R   K  + L  +++N + +V 
Sbjct: 238 SALREQHTKTLATIAKHGRSGKRAKDQIAQLADIFKQFRLVPKQFDTLVLSMKNMMKRVR 297

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
             E+Q+ +++V+  GMP+  F  +   N  +  WV    K    +   L +    I+   
Sbjct: 298 AEERQLQKVLVDIAGMPKDEFEALIVANGSSDAWVAKALKSTKAWAKRLPKYEERIRLSL 357

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
             L N++    L +  +R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 358 DNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQF 417

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 418 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 477

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGD
Sbjct: 478 KLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGD 537

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFD
Sbjct: 538 FIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 597

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKLR
Sbjct: 598 VTRERIRQIEAKALRKLR 615


>gi|381170700|ref|ZP_09879854.1| RNA polymerase sigma factor RpoD [Xanthomonas citri pv.
            mangiferaeindicae LMG 941]
 gi|380688752|emb|CCG36341.1| RNA polymerase sigma factor RpoD [Xanthomonas citri pv.
            mangiferaeindicae LMG 941]
          Length = 625

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 404/612 (66%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V      + ++    +  +A+           E  ++  N++  + K +K + K G 
Sbjct: 192  PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVAMRMENLANEYAKFKKVYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  541 bits (1394), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 394/599 (65%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V      + ++    +  +A+           E  ++  N++  + K +K + K G 
Sbjct: 192 PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVAMRMENLANEYAKFKKVYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|410719475|gb|AFV80118.1| RNA polymerase sigma factor [Xanthomonas arboricola]
 gi|410719477|gb|AFV80119.1| RNA polymerase sigma factor [Xanthomonas arboricola]
          Length = 624

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/611 (50%), Positives = 408/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  541 bits (1394), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 300/598 (50%), Positives = 398/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|384421006|ref|YP_005630366.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzicola
            BLS256]
 gi|353463919|gb|AEQ98198.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzicola
            BLS256]
          Length = 624

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 306/611 (50%), Positives = 407/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D      E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDAAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  541 bits (1393), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 299/598 (50%), Positives = 397/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D      E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDAAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  + ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSMEMEKASYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|145630289|ref|ZP_01786070.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260582763|ref|ZP_05850550.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
 gi|144984024|gb|EDJ91461.1| aspartate ammonia-lyase [Haemophilus influenzae R3021]
 gi|260094213|gb|EEW78114.1| aspartate ammonia-lyase [Haemophilus influenzae NT127]
          Length = 629

 Score =  556 bits (1434), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/637 (48%), Positives = 417/637 (65%), Gaps = 35/637 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 993
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------K 1036
               +N + +   N ++E+   ESS+AD+   + E+                        K
Sbjct: 180  IEEHNGLDEDFSNEDDEE---ESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREK 236

Query: 1037 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRN 1091
            F  +     K     EK G + +   +A + I+  +LG      R   K  + L  +++ 
Sbjct: 237  FQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKE 291

Query: 1092 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 1151
             + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +   
Sbjct: 292  MMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYED 351

Query: 1152 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
             I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 352  RIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYT 411

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 412  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 471

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+
Sbjct: 472  MIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDD 531

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 532  DSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEE 591

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 592  VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  541 bits (1395), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 300/624 (48%), Positives = 408/624 (65%), Gaps = 35/624 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 203
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-----------------K 246
              +N + +   N ++E+   ESS+AD+   + E+                        K
Sbjct: 180 IEEHNGLDEDFSNEDDEE---ESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREK 236

Query: 247 FSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRN 301
           F  +     K     EK G + +   +A + I+  +LG      R   K  + L  +++ 
Sbjct: 237 FQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKE 291

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIP 361
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +   
Sbjct: 292 MMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYED 351

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
            I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT
Sbjct: 352 RIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYT 411

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 412 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 471

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+
Sbjct: 472 MIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDD 531

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEE
Sbjct: 532 DSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEE 591

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VGKQFDVTRERIRQIEAKALRKLR
Sbjct: 592 VGKQFDVTRERIRQIEAKALRKLR 615


>gi|418515511|ref|ZP_13081691.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            malvacearum str. GSPB1386]
 gi|410707809|gb|EKQ66259.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            malvacearum str. GSPB1386]
          Length = 625

 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 403/612 (65%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192  PVAVSGDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  541 bits (1393), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 393/599 (65%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192 PVAVSGDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|294666254|ref|ZP_06731505.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp. aurantifolii
            str. ICPB 10535]
 gi|292603963|gb|EFF47363.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp. aurantifolii
            str. ICPB 10535]
          Length = 625

 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 403/612 (65%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192  PVAVSDDEAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  540 bits (1392), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 393/599 (65%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192 PVAVSDDEAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|21244512|ref|NP_644094.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. citri
            str. 306]
 gi|390990489|ref|ZP_10260774.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. punicae
            str. LMG 859]
 gi|418522015|ref|ZP_13088054.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            malvacearum str. GSPB2388]
 gi|32130007|sp|Q8PG33.1|RPOD_XANAC RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|21110182|gb|AAM38630.1| RNA polymerase sigma-70 factor [Xanthomonas axonopodis pv. citri str.
            306]
 gi|372554812|emb|CCF67749.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. punicae
            str. LMG 859]
 gi|410701639|gb|EKQ60157.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv.
            malvacearum str. GSPB2388]
          Length = 625

 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 403/612 (65%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192  PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  540 bits (1392), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 393/599 (65%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V      + ++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192 PVAVSDDEAVDEDDDEDGDDEAAEEEAGPTGPDPVEVATRMENLANEYAKFKKVYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIISEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|188993312|ref|YP_001905322.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
            campestris str. B100]
 gi|167735072|emb|CAP53284.1| RNA polymerase sigma-70 factor [Xanthomonas campestris pv.
            campestris]
          Length = 624

 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 307/611 (50%), Positives = 408/611 (66%), Gaps = 15/611 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132  EEGLSQVQAALGVFPLSTELLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 1057
                +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192  PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252  HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312  FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372  SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492  ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 552  ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 611

Query: 1418 SRYYKLKIFLE 1428
            SR  +L+ FL+
Sbjct: 612  SRSEQLRSFLD 622



 Score =  540 bits (1392), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 300/598 (50%), Positives = 398/598 (66%), Gaps = 15/598 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+   P +   +L   +   + + ++ EIV G   LI++  ++   +    
Sbjct: 132 EEGLSQVQAALGVFPLSTELLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKLK-------YESLIKFSNISFHFDKMRKAFEKEGYN 267
               +E  + E    D   +  E+          E   +  N++  + K +K + K G  
Sbjct: 192 PVAVDEDAVDEDDDEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGAE 251

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR  
Sbjct: 252 HKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATTVARMPRKD 311

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++I
Sbjct: 312 FIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKEI 371

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           +R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 372 SRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 431

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P 
Sbjct: 432 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++ 
Sbjct: 492 ELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINLS 551

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 ETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 609


>gi|325924346|ref|ZP_08185890.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
            19865]
 gi|325545211|gb|EGD16521.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthomonas gardneri ATCC
            19865]
          Length = 625

 Score =  556 bits (1432), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 304/612 (49%), Positives = 406/612 (66%), Gaps = 16/612 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 996
            EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132  EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
               V + +  ++++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192  PVAVSEDDAADDDDAEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGA 251

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
              +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252  EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATAVARMPRK 311

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312  DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKE 371

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372  ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492  EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
               V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRH
Sbjct: 552  SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 611

Query: 1417 PSRYYKLKIFLE 1428
            PSR  +L+ FL+
Sbjct: 612  PSRSEQLRSFLD 623



 Score =  540 bits (1391), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 396/599 (66%), Gaps = 16/599 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NITSDD-----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  + +        E   AAL+ +D++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID-----------KNFSS 206
           EEGL  +  A+   P +   +L   +   + + ++ EIV G  D              + 
Sbjct: 132 EEGLSQVQAALGVFPLSTEMLLADYEAHKEGKKRLAEIVVGFNDLIEEADAAAAALAAAG 191

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
              V + +  ++++    +  +A+           E   +  N++  + K +K + K G 
Sbjct: 192 PVAVSEDDAADDDDAEDGDDDAAEEEAGPTGPDPVEVATRMENLANEYAKFKKIYAKNGA 251

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
             +  +KA  +++     ++      + L   LR  +N +   E+++L +      MPR 
Sbjct: 252 EHKLVVKAREDMAAIFTTLKLPLPLTDALVTQLRGVVNGIKDHERKVLHLATAVARMPRK 311

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            FI+ +  N+ NL WV++  K +  ++  L      I   QQ  I ++    L L ++++
Sbjct: 312 DFIRSWEGNQTNLEWVEDALKRKQKWSSALRDVKDQIVSEQQGSIEMEKANYLTLGEIKE 371

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           I+R M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 372 ISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 431

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P
Sbjct: 432 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQFGREATP 491

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             +A +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P D   N ++
Sbjct: 492 EELAKEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIDNTTNINL 551

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
              V+D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 SETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 610


>gi|90416498|ref|ZP_01224429.1| RNA polymerase sigma factor RpoD [gamma proteobacterium HTCC2207]
 gi|90331697|gb|EAS46925.1| RNA polymerase sigma factor RpoD [gamma proteobacterium HTCC2207]
          Length = 612

 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 299/606 (49%), Positives = 408/606 (67%), Gaps = 16/606 (2%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL--M 890
             K LI  G+E+ YLT++E+ND LPEDI D E +E II+    M I+V E   D +TL  +
Sbjct: 12   IKDLIAKGREQRYLTYAEVNDHLPEDIADPEQVEDIIQMINDMGITVFETAPDADTLSSL 71

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
             S+ T D+       AAL++V+S+  RT DP++MYMREMGSVELLTR+GEIEIAKRIEEG
Sbjct: 72   ASDNTPDEVAAAEAAAALASVESEQHRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEG 131

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
             ++++ A++  PTT+  I+   +K+   E K+ +I+ G ++         +       + 
Sbjct: 132  TRELMSAVADWPTTVATIVAEYEKVEAGEKKLTDIISGYLNPMEH-----VPSALAQQQA 186

Query: 1011 KILIESSSADLSTEQLEKLKYESLIKFSNISF-HFDKMRKAFEKE-------GYNSESYI 1062
               ++  + +   E+ E+ ++E  +    ++F  FD +RK  +K        G   E+  
Sbjct: 187  AEALKLENGEEEEEEEEEEQHEGGLD-PEVAFERFDTIRKQLKKTDTCIARYGRGGEASQ 245

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            K    ++     ++ T +  + L   +R  + +V   E++I+ + +    MPR  FIK+F
Sbjct: 246  KNLEELAELFKYLKLTPRQFDPLIAKVRLAVERVRAEERKIMRLCIRLGKMPRKDFIKMF 305

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
            P NE N+ W     K +  +   +      I   Q+KL  ++    + +  ++DINR+M 
Sbjct: 306  PGNESNMQWTAELAKSKESWAERVSAQEVEILRSQRKLAQVEKLADMNIAQIKDINRRMT 365

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE  AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 366  MGEAMARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +
Sbjct: 426  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPEELAER 485

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            MEMPE+KIRK++KIAKEP+SME+P+G+DED+ +GD IED  +  P D A   ++    + 
Sbjct: 486  MEMPEDKIRKVLKIAKEPISMETPIGEDEDASIGDLIEDTTIALPLDEATKNNLTESTRG 545

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   
Sbjct: 546  VLSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDH 605

Query: 1423 LKIFLE 1428
            L+ F++
Sbjct: 606  LRSFID 611



 Score =  543 bits (1400), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 297/601 (49%), Positives = 402/601 (66%), Gaps = 17/601 (2%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL--M 100
            K LI  G+E+ YLT++E+ND LPEDI D E +E II+    M I+V E   D +TL  +
Sbjct: 12  IKDLIAKGREQRYLTYAEVNDHLPEDIADPEQVEDIIQMINDMGITVFETAPDADTLSSL 71

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
            S+ T D+       AAL++V+S+  RT DP++MYMREMGSVELLTR+GEIEIAKRIEEG
Sbjct: 72  ASDNTPDEVAAAEAAAALASVESEQHRTTDPVRMYMREMGSVELLTREGEIEIAKRIEEG 131

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
            ++++ A++  PTT+  I+   +K+   E K+ +I+ G ++         +       + 
Sbjct: 132 TRELMSAVADWPTTVATIVAEYEKVEAGEKKLTDIISGYLNPMEH-----VPSALAQQQA 186

Query: 221 KILIESSSADLSTEQLEKLKYESLIKFSNISF-HFDKMRKAFEKE-------GYNSESYI 272
              ++  + +   E+ E+ ++E  +    ++F  FD +RK  +K        G   E+  
Sbjct: 187 AEALKLENGEEEEEEEEEEQHEGGLD-PEVAFERFDTIRKQLKKTDTCIARYGRGGEASQ 245

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           K    ++     ++ T +  + L   +R  + +V   E++I+ + +    MPR  FIK+F
Sbjct: 246 KNLEELAELFKYLKLTPRQFDPLIAKVRLAVERVRAEERKIMRLCIRLGKMPRKDFIKMF 305

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
           P NE N+ W     K +  +   +      I   Q+KL  ++    + +  ++DINR+M 
Sbjct: 306 PGNESNMQWTAELAKSKESWAERVSAQEVEILRSQRKLAQVEKLADMNIAQIKDINRRMT 365

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE  AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 366 MGEAMARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ+LQE G EP P  +A +
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPSPEELAER 485

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           MEMPE+KIRK++KIAKEP+SME+P+G+DED+ +GD IED  +  P D A   ++    + 
Sbjct: 486 MEMPEDKIRKVLKIAKEPISMETPIGEDEDASIGDLIEDTTIALPLDEATKNNLTESTRG 545

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDW 631
           +L+SLT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D 
Sbjct: 546 VLSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDH 605

Query: 632 L 632
           L
Sbjct: 606 L 606


>gi|380510259|ref|ZP_09853666.1| RNA polymerase sigma factor RpoD [Xanthomonas sacchari NCPPB 4393]
          Length = 620

 Score =  555 bits (1431), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 303/607 (49%), Positives = 406/607 (66%), Gaps = 11/607 (1%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +    V   +
Sbjct: 132  EEGLGQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPPVAVSDDD 191

Query: 1005 KNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
               + +    +    D + E          E   +   ++  + K +KA  K G   +  
Sbjct: 192  SATDADADEDDDEDVDTAEEDAGPTGPDPAEVARRMEVLATEYAKFKKAHAKNGAEHKLV 251

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
             K  N+I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ 
Sbjct: 252  TKLRNDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRS 311

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            +  N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M
Sbjct: 312  WEGNQTNVAWVDDALKRKQKWSSALRDVKDQIIAEQEATVAVEQATYLSLAELKEISRAM 371

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372  AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 432  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 491

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+
Sbjct: 492  EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVR 551

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  
Sbjct: 552  DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 611

Query: 1422 KLKIFLE 1428
            +L+ FL+
Sbjct: 612  QLRSFLD 618



 Score =  540 bits (1391), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 296/594 (49%), Positives = 396/594 (66%), Gaps = 11/594 (1%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKQLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +    V   +
Sbjct: 132 EEGLGQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPPVAVSDDD 191

Query: 215 KNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
              + +    +    D + E          E   +   ++  + K +KA  K G   +  
Sbjct: 192 SATDADADEDDDEDVDTAEEDAGPTGPDPAEVARRMEVLATEYAKFKKAHAKNGAEHKLV 251

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
            K  N+I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ 
Sbjct: 252 TKLRNDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRS 311

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           +  N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M
Sbjct: 312 WEGNQTNVAWVDDALKRKQKWSSALRDVKDQIIAEQEATVAVEQATYLSLAELKEISRAM 371

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 372 AYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A 
Sbjct: 432 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAK 491

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+
Sbjct: 492 EMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVR 551

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 DVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|433679695|ref|ZP_20511396.1| RNA polymerase sigma factor rpoD [Xanthomonas translucens pv.
            translucens DSM 18974]
 gi|430815194|emb|CCP42001.1| RNA polymerase sigma factor rpoD [Xanthomonas translucens pv.
            translucens DSM 18974]
          Length = 619

 Score =  555 bits (1429), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 300/606 (49%), Positives = 402/606 (66%), Gaps = 10/606 (1%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +        +
Sbjct: 132  EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPAVVASDDD 191

Query: 1005 KNNNEEKILIESSSADLSTEQ--LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
               +      +        E         E   +   ++  + K +KA  K G   +   
Sbjct: 192  SAADASDDDDDEEVEAAEEEAGPTGPDPAEVARRMELLATEYAKFKKAHAKNGAEHKLVT 251

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            K   +I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ +
Sbjct: 252  KLRTDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 311

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M 
Sbjct: 312  EGNQTNVAWVDDALKRKQKWSSALRDVKDQIVSEQEATVAVEQATYLSLTELKEISRAMA 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A +
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+D
Sbjct: 492  MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +
Sbjct: 552  VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 611

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 612  LRSFLD 617



 Score =  539 bits (1388), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 293/593 (49%), Positives = 392/593 (66%), Gaps = 10/593 (1%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +        +
Sbjct: 132 EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPAVVASDDD 191

Query: 215 KNNNEEKILIESSSADLSTEQ--LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
              +      +        E         E   +   ++  + K +KA  K G   +   
Sbjct: 192 SAADASDDDDDEEVEAAEEEAGPTGPDPAEVARRMELLATEYAKFKKAHAKNGAEHKLVT 251

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           K   +I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ +
Sbjct: 252 KLRTDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 311

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M 
Sbjct: 312 EGNQTNVAWVDDALKRKQKWSSALRDVKDQIVSEQEATVAVEQATYLSLTELKEISRAMA 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A +
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+D
Sbjct: 492 MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|262378901|ref|ZP_06072058.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
            SH164]
 gi|421466075|ref|ZP_15914761.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
            WC-A-157]
 gi|421855871|ref|ZP_16288244.1| RNA polymerase sigma-D factor [Acinetobacter radioresistens DSM 6976
            = NBRC 102413]
 gi|262300186|gb|EEY88098.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
            SH164]
 gi|400203586|gb|EJO34572.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens
            WC-A-157]
 gi|403188704|dbj|GAB74445.1| RNA polymerase sigma-D factor [Acinetobacter radioresistens DSM 6976
            = NBRC 102413]
          Length = 629

 Score =  555 bits (1429), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/614 (48%), Positives = 412/614 (67%), Gaps = 21/614 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  +  
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIK---------- 1002
            ++H+I+  P  +  +L       + E ++ +I+ G +D         VI+          
Sbjct: 134  VLHSIAYWPNAVEVVLKEYKDYQEGERRLADILSGYLDPESDEEIPEVIEDAVLEEDEDE 193

Query: 1003 -GNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEG 1055
              +K+  E K+  +    + S    +           + ++F+ +   + + +   EK G
Sbjct: 194  TASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAKVRFTELETVWQETKSVIEKHG 253

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +S     A   +++  +  +FT +  + + + +R    Q+   E++I+   V +  M R
Sbjct: 254  RDSAEAKAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDR 313

Query: 1116 LHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
              F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D+
Sbjct: 314  TQFRTSFPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDI 373

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 374  KDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 433

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP
Sbjct: 434  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREP 493

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA + 
Sbjct: 494  TPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSE 553

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 554  GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 613

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FLE
Sbjct: 614  RHPSRSEHLRSFLE 627



 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 289/601 (48%), Positives = 403/601 (67%), Gaps = 21/601 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  +  
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIK---------- 212
           ++H+I+  P  +  +L       + E ++ +I+ G +D         VI+          
Sbjct: 134 VLHSIAYWPNAVEVVLKEYKDYQEGERRLADILSGYLDPESDEEIPEVIEDAVLEEDEDE 193

Query: 213 -GNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEG 265
             +K+  E K+  +    + S    +           + ++F+ +   + + +   EK G
Sbjct: 194 TASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAKVRFTELETVWQETKSVIEKHG 253

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +S     A   +++  +  +FT +  + + + +R    Q+   E++I+   V +  M R
Sbjct: 254 RDSAEAKAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDR 313

Query: 326 LHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
             F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D+
Sbjct: 314 TQFRTSFPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDI 373

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 374 KDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 433

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP
Sbjct: 434 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREP 493

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA + 
Sbjct: 494 TPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSE 553

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 554 GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 613

Query: 625 R 625
           R
Sbjct: 614 R 614


>gi|255318840|ref|ZP_05360066.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens SK82]
 gi|255304096|gb|EET83287.1| RNA polymerase sigma factor RpoD [Acinetobacter radioresistens SK82]
          Length = 626

 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/614 (48%), Positives = 412/614 (67%), Gaps = 21/614 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  +  
Sbjct: 11   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 70

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIK---------- 1002
            ++H+I+  P  +  +L       + E ++ +I+ G +D         VI+          
Sbjct: 131  VLHSIAYWPNAVEVVLKEYKDYQEGERRLADILSGYLDPESDEEIPEVIEDAVLEEDEDE 190

Query: 1003 -GNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEG 1055
              +K+  E K+  +    + S    +           + ++F+ +   + + +   EK G
Sbjct: 191  TASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAKVRFTELETVWQETKSVIEKHG 250

Query: 1056 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 1115
             +S     A   +++  +  +FT +  + + + +R    Q+   E++I+   V +  M R
Sbjct: 251  RDSAEAKAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDR 310

Query: 1116 LHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 1174
              F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D+
Sbjct: 311  TQFRTSFPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDI 370

Query: 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 1234
            +DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 371  KDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 430

Query: 1235 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294
            FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP
Sbjct: 431  FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREP 490

Query: 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 1354
             P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA + 
Sbjct: 491  TPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSE 550

Query: 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414
             ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 551  GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 610

Query: 1415 RHPSRYYKLKIFLE 1428
            RHPSR   L+ FLE
Sbjct: 611  RHPSRSEHLRSFLE 624



 Score =  538 bits (1387), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 289/601 (48%), Positives = 403/601 (67%), Gaps = 21/601 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN-- 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M  +  
Sbjct: 11  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDAMFEDNA 70

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 71  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 130

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN-NRVIK---------- 212
           ++H+I+  P  +  +L       + E ++ +I+ G +D         VI+          
Sbjct: 131 VLHSIAYWPNAVEVVLKEYKDYQEGERRLADILSGYLDPESDEEIPEVIEDAVLEEDEDE 190

Query: 213 -GNKNNNEEKILIESSSADLSTEQLEKLKYE------SLIKFSNISFHFDKMRKAFEKEG 265
             +K+  E K+  +    + S    +           + ++F+ +   + + +   EK G
Sbjct: 191 TASKSTKEVKLDDDEEEEEESESDDDSEADSGPDPEIAKVRFTELETVWQETKSVIEKHG 250

Query: 266 YNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPR 325
            +S     A   +++  +  +FT +  + + + +R    Q+   E++I+   V +  M R
Sbjct: 251 RDSAEAKAALEALASVFMMFKFTPRLFDIISEMIRGTHEQIRTSEREIMRYAVRRGRMDR 310

Query: 326 LHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDL 384
             F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L + D+
Sbjct: 311 TQFRTSFPGQESNPGWLDEQMAKASPDIKGHLEKVRPDVLAFQQKIADIEKELGLNVIDI 370

Query: 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDK 444
           +DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDK
Sbjct: 371 KDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 430

Query: 445 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 504
           FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE G EP
Sbjct: 431 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEMGREP 490

Query: 505 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNA 564
            P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P DAA + 
Sbjct: 491 TPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSPVDAATSE 550

Query: 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624
            ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKALRKL
Sbjct: 551 GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 610

Query: 625 R 625
           R
Sbjct: 611 R 611


>gi|375135780|ref|YP_004996430.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
            during exponential growth [Acinetobacter calcoaceticus
            PHEA-2]
 gi|325123225|gb|ADY82748.1| sigma D (sigma 70) factor of RNA polymerase , major sigma factor
            during exponential growth [Acinetobacter calcoaceticus
            PHEA-2]
          Length = 636

 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 294/621 (47%), Positives = 412/621 (66%), Gaps = 28/621 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 893
            LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14   LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
              +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 1001
            ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134  VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 1056
              +K+  E K+  +    +   +   +         + ++F+ +   + K +   EK G 
Sbjct: 194  SSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFTELEAAWAKTKAVVEKHGR 253

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254  NSPEAEEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 1117 HFIKVFPENEI--------NLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDI 1167
             F   FP++E         N  W+D +  K   +    L +  P +   QQK+ +++ ++
Sbjct: 314  QFRTSFPKHESTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKEL 373

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 374  SLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 433

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+L
Sbjct: 434  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLL 493

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
            QE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P
Sbjct: 494  QEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSP 553

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIE
Sbjct: 554  IDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIE 613

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKLRHPSR   L+ FLE
Sbjct: 614  AKALRKLRHPSRSEHLRSFLE 634



 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 286/608 (47%), Positives = 403/608 (66%), Gaps = 28/608 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML--SN 103
           LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   +++  M   S 
Sbjct: 14  LISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAPESDDTMFGESA 73

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
             +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  DATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN------------NRVI 211
           ++++I+  P  +  +L   +     E ++ +I+ G +D     +                
Sbjct: 134 VLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPETDEDIPEVLEEVEELEEEDE 193

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKFSNISFHFDKMRKAFEKEGY 266
             +K+  E K+  +    +   +   +         + ++F+ +   + K +   EK G 
Sbjct: 194 SSSKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRFTELEAAWAKTKAVVEKHGR 253

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           NS    +A   ++   +  +FT +  + + + +R    Q+   E++I+   V +  M R 
Sbjct: 254 NSPEAEEALEALATVFMMFKFTPRLFDIISEMIRGTHEQIRANEREIMRYAVRRGRMDRT 313

Query: 327 HFIKVFPENEI--------NLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDI 377
            F   FP++E         N  W+D +  K   +    L +  P +   QQK+ +++ ++
Sbjct: 314 QFRTSFPKHESTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAFQQKIADIEKEL 373

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 374 SLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 433

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+L
Sbjct: 434 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLL 493

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
           QE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED+N+ +P
Sbjct: 494 QEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDQNITSP 553

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIE
Sbjct: 554 IDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIE 613

Query: 618 AKALRKLR 625
           AKALRKLR
Sbjct: 614 AKALRKLR 621


>gi|190575994|ref|YP_001973839.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia K279a]
 gi|424670307|ref|ZP_18107332.1| RNA polymerase sigma factor rpoD [Stenotrophomonas maltophilia
            Ab55555]
 gi|190013916|emb|CAQ47556.1| putative RNA polymerase sigma factor RpoD [Stenotrophomonas
            maltophilia K279a]
 gi|401070765|gb|EJP79279.1| RNA polymerase sigma factor rpoD [Stenotrophomonas maltophilia
            Ab55555]
 gi|456734989|gb|EMF59759.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia EPM1]
          Length = 617

 Score =  554 bits (1428), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 308/608 (50%), Positives = 406/608 (66%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKG 1003
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G   L+D+  +        
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLVDEEPAPPAVAADD 189

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            + + + E    E    D   E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190  SADADAEGDEDEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248  LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WV++  K +  ++  L      I   QQ  I+++T   L L +L++I+R 
Sbjct: 308  SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIETLTQLDLEELKEISRA 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
             +L+ FL+
Sbjct: 608  EQLRSFLD 615



 Score =  538 bits (1387), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 301/595 (50%), Positives = 396/595 (66%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKG 213
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G   L+D+  +        
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLVDEEPAPPAVAADD 189

Query: 214 NKNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           + + + E    E    D   E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190 SADADAEGDEDEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248 LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WV++  K +  ++  L      I   QQ  I+++T   L L +L++I+R 
Sbjct: 308 SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIETLTQLDLEELKEISRA 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|90020363|ref|YP_526190.1| Fis family transcriptional regulator [Saccharophagus degradans 2-40]
 gi|89949963|gb|ABD79978.1| RNA polymerase sigma factor RpoD-like protein [Saccharophagus
            degradans 2-40]
          Length = 613

 Score =  554 bits (1427), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 301/604 (49%), Positives = 400/604 (66%), Gaps = 8/604 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G+E+GYLT+ E+ND LP+DI D + +E II+    M I V E   D + L++
Sbjct: 10   RIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDADELLM 69

Query: 892  SNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            ++  S  D   A EAA +    +   GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TDGDSSADEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            GL+++ HAI+  P  + + +   D + K E ++ +++ G +D        V+      + 
Sbjct: 130  GLRELNHAIALWPEAVQQYVNEYDLVEKEERRLADVISGWLDPAEDVAPPVVAAETAEDT 189

Query: 1010 EKILIESSSADLSTEQLEKL-----KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 1064
            +    +    D  TE  E+      +Y +  +F  +     K+ KA  K G+ S++  K 
Sbjct: 190  DSDDDDDDDDDTDTEDEEESTGIDPEY-ARERFDELKAALLKVEKAIAKHGFESKAAGKE 248

Query: 1065 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 1124
               +       +   +  + +   +R  + +V   E++I+ +     GMPR  F+K FP 
Sbjct: 249  MEALGEIFKYFKLPPRQFDPIYQGIRQILTRVRAEEREIMRLCTRLGGMPRKTFMKEFPG 308

Query: 1125 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 1184
             E + +W+        DY+  L      I   Q+KL  +Q +  L L  +++INR+M  G
Sbjct: 309  QETDEDWIPATIGKGRDYSDSLKPYAEDIIRAQRKLKQIQEESGLSLGHIKEINRRMSIG 368

Query: 1185 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244
            E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 369  EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

Query: 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 1304
            TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 429  TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 488

Query: 1305 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 1364
            MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    +    + +L
Sbjct: 489  MPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPVDSATIQGLTEATRSVL 548

Query: 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424
              LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+
Sbjct: 549  AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDHLR 608

Query: 1425 IFLE 1428
             FL+
Sbjct: 609  GFLD 612



 Score =  540 bits (1391), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 294/591 (49%), Positives = 391/591 (66%), Gaps = 8/591 (1%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G+E+GYLT+ E+ND LP+DI D + +E II+    M I V E   D + L++
Sbjct: 10  RIKELINRGREQGYLTYDEVNDHLPDDISDPDQVEDIIQMINDMGIRVYEVAPDADELLM 69

Query: 102 SNITSDDDVEEATEAALSTVDSDF--GRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           ++  S  D   A EAA +    +   GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TDGDSSADEIAAAEAAAALAAVETEAGRTTDPVRMYMREMGTVELLTREGEIAIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           GL+++ HAI+  P  + + +   D + K E ++ +++ G +D        V+      + 
Sbjct: 130 GLRELNHAIALWPEAVQQYVNEYDLVEKEERRLADVISGWLDPAEDVAPPVVAAETAEDT 189

Query: 220 EKILIESSSADLSTEQLEKL-----KYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKA 274
           +    +    D  TE  E+      +Y +  +F  +     K+ KA  K G+ S++  K 
Sbjct: 190 DSDDDDDDDDDTDTEDEEESTGIDPEY-ARERFDELKAALLKVEKAIAKHGFESKAAGKE 248

Query: 275 HNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPE 334
              +       +   +  + +   +R  + +V   E++I+ +     GMPR  F+K FP 
Sbjct: 249 MEALGEIFKYFKLPPRQFDPIYQGIRQILTRVRAEEREIMRLCTRLGGMPRKTFMKEFPG 308

Query: 335 NEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAG 394
            E + +W+        DY+  L      I   Q+KL  +Q +  L L  +++INR+M  G
Sbjct: 309 QETDEDWIPATIGKGRDYSDSLKPYAEDIIRAQRKLKQIQEESGLSLGHIKEINRRMSIG 368

Query: 395 EMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454
           E +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS
Sbjct: 369 EARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

Query: 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKME 514
           TYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +ME
Sbjct: 429 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERME 488

Query: 515 MPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDIL 574
           MPE+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    +    + +L
Sbjct: 489 MPEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPVDSATIQGLTEATRSVL 548

Query: 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 549 AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599


>gi|424793209|ref|ZP_18219350.1| RNA polymerase sigma-70 factor [Xanthomonas translucens pv. graminis
            ART-Xtg29]
 gi|422796740|gb|EKU25196.1| RNA polymerase sigma-70 factor [Xanthomonas translucens pv. graminis
            ART-Xtg29]
          Length = 619

 Score =  553 bits (1426), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 299/606 (49%), Positives = 402/606 (66%), Gaps = 10/606 (1%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12   IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 893  NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72   DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 1004
            EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +        +
Sbjct: 132  EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPAVVASDDD 191

Query: 1005 KNNNEEKILIESSSADLSTEQ--LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 1062
               +      +        E         E   +   ++  + K +KA  + G   +   
Sbjct: 192  SAADASDDDDDEEVEAAEEEAGPTGPDPAEVARRMELLATEYAKFKKAHARNGAEHKLVT 251

Query: 1063 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 1122
            K   +I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ +
Sbjct: 252  KLRTDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 311

Query: 1123 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 1182
              N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M 
Sbjct: 312  EGNQTNVAWVDDALKRKQKWSSALRDVKDQIVSEQEATVAVEQATYLSLTELKEISRAMA 371

Query: 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242
             GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372  YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 1302
            FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A +
Sbjct: 432  FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 491

Query: 1303 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 1362
            M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+D
Sbjct: 492  MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 551

Query: 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422
            +L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +
Sbjct: 552  VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQ 611

Query: 1423 LKIFLE 1428
            L+ FL+
Sbjct: 612  LRSFLD 617



 Score =  538 bits (1385), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 292/593 (49%), Positives = 392/593 (66%), Gaps = 10/593 (1%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K+LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L+
Sbjct: 12  IKLLISKGLEQGYLTYAEVNDHLPDDLVDPEQIEDIISMINGMGIDVHEVAPDAETLLLN 71

Query: 103 NI-TSDDDVEEATEAALSTVDS----DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +  T + +V++      +   +    + GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 72  DGNTGNREVDDTAAEEAAAALTALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKRI 131

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKGN 214
           EEGL  +  A+ + P  +  +L   ++  + + ++ EIV G   LI++  +        +
Sbjct: 132 EEGLSQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPAVVASDDD 191

Query: 215 KNNNEEKILIESSSADLSTEQ--LEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYI 272
              +      +        E         E   +   ++  + K +KA  + G   +   
Sbjct: 192 SAADASDDDDDEEVEAAEEEAGPTGPDPAEVARRMELLATEYAKFKKAHARNGAEHKLVT 251

Query: 273 KAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF 332
           K   +I+   + ++      + L   LR+ + QV   E+++L +  +   MPR  FI+ +
Sbjct: 252 KLRTDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARMPRKDFIRSW 311

Query: 333 PENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMI 392
             N+ N+ WVD+  K +  ++  L      I   Q+  + ++    L L +L++I+R M 
Sbjct: 312 EGNQTNVAWVDDALKRKQKWSSALRDVKDQIVSEQEATVAVEQATYLSLTELKEISRAMA 371

Query: 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452
            GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK
Sbjct: 372 YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIK 512
           FSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A +
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELAKE 491

Query: 513 MEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKD 572
           M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V+D
Sbjct: 492 MDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETVRD 551

Query: 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 552 VLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|254281823|ref|ZP_04956791.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma proteobacterium
            NOR51-B]
 gi|219678026|gb|EED34375.1| RNA polymerase, sigma 70 subunit, RpoD family [gamma proteobacterium
            NOR51-B]
          Length = 603

 Score =  553 bits (1425), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 298/607 (49%), Positives = 409/607 (67%), Gaps = 24/607 (3%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT+SE+ND LP+DI + + +E II+    M I V E   D + L+L
Sbjct: 10   RLKALIAKGKEQGYLTYSEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELIL 69

Query: 892  S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            +  + ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFSSNNRVI 1001
            G+++++ A++  P     +    D ++K E K+ +I+ G +D        +  +      
Sbjct: 130  GIRELMAAMAHYPGVARRLTEEYDLVTKEERKLADILVGYLDPADHVPSAQEIAEQTAAA 189

Query: 1002 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 1061
            K NK +++E       + D   + +E  K     +F+ +     +  K    E   S+  
Sbjct: 190  K-NKTDDDE-------APDTGPDPIEAKK-----RFTALKRQCTRTEKVLAAESRQSKKA 236

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            I   + +       + T +  + L +  R  +  V + E++I+ IVV +C M R  FIK 
Sbjct: 237  IAEMDKLGELFKFFKLTPRVFDPLVEAPRTALQIVREQEREIMRIVVRECRMDRKDFIKS 296

Query: 1122 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 1181
            F  +E +  WV    + + +    +  +   I+ LQ+++  ++ +I L + ++++INR+M
Sbjct: 297  FQGSESDSRWVSRVMR-KKELGARISLHKDEIQRLQRRIGAVEDEIGLTVAEIKEINRRM 355

Query: 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 1241
              GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 356  SMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 415

Query: 1242 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301
            KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 416  KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 475

Query: 1302 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 1361
            +MEMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A    +     
Sbjct: 476  RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVDSATEEGLTEATT 535

Query: 1362 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421
            D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R  
Sbjct: 536  DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 595

Query: 1422 KLKIFLE 1428
             L+ FL+
Sbjct: 596  YLRSFLD 602



 Score =  543 bits (1398), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 295/602 (49%), Positives = 404/602 (67%), Gaps = 25/602 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT+SE+ND LP+DI + + +E II+    M I V E   D + L+L
Sbjct: 10  RLKALIAKGKEQGYLTYSEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELIL 69

Query: 102 S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           +  + ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--------KNFSSNNRVI 211
           G+++++ A++  P     +    D ++K E K+ +I+ G +D        +  +      
Sbjct: 130 GIRELMAAMAHYPGVARRLTEEYDLVTKEERKLADILVGYLDPADHVPSAQEIAEQTAAA 189

Query: 212 KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESY 271
           K NK +++E       + D   + +E  K     +F+ +     +  K    E   S+  
Sbjct: 190 K-NKTDDDE-------APDTGPDPIEAKK-----RFTALKRQCTRTEKVLAAESRQSKKA 236

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           I   + +       + T +  + L +  R  +  V + E++I+ IVV +C M R  FIK 
Sbjct: 237 IAEMDKLGELFKFFKLTPRVFDPLVEAPRTALQIVREQEREIMRIVVRECRMDRKDFIKS 296

Query: 332 FPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKM 391
           F  +E +  WV    + + +    +  +   I+ LQ+++  ++ +I L + ++++INR+M
Sbjct: 297 FQGSESDSRWVSRVMR-KKELGARISLHKDEIQRLQRRIGAVEDEIGLTVAEIKEINRRM 355

Query: 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 451
             GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGY
Sbjct: 356 SMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 415

Query: 452 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511
           KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  
Sbjct: 416 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGE 475

Query: 512 KMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVK 571
           +MEMPE+K+RK++KIAKEP+SME+P+GDDEDS LGDFIED  + +P D+A    +     
Sbjct: 476 RMEMPEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDVTIASPVDSATEEGLTEATT 535

Query: 572 DILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHD 630
           D+L  LT RE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D
Sbjct: 536 DVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 595

Query: 631 WL 632
           +L
Sbjct: 596 YL 597


>gi|325576583|ref|ZP_08147301.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
            parainfluenzae ATCC 33392]
 gi|325161146|gb|EGC73261.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus
            parainfluenzae ATCC 33392]
          Length = 629

 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/635 (46%), Positives = 411/635 (64%), Gaps = 31/635 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1    MEQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQHDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N +
Sbjct: 120  TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLDHYDQVEAGNYRLADLITGFVDPNIA 179

Query: 996  SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------- 1035
                       N +E    E  SA+ + +  ++   E                       
Sbjct: 180  EEETA------NIDEHFADEDESAESAVDVDDESDEEDESDSSSSSDDSDSDNSIDPEVA 233

Query: 1036 --KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
              +F+ +     K      K G + +        +++     R   K  + L  +++N I
Sbjct: 234  RERFAALREQHTKTLATIAKHGRSGKRAKDQIAQLADIFKQFRLVPKQFDVLVLSMKNMI 293

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
             +V   E+Q+ +++V+  GMP+  F  +   N  N  WV    K    +   L +    I
Sbjct: 294  KRVRAEERQLQKVLVDIAGMPKDEFEALIVANGSNDTWVAKALKSTKAWAKRLPKYEERI 353

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            +     L N++    L +  +R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+R
Sbjct: 354  RLSLDNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNR 413

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 414  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 473

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DS
Sbjct: 474  ETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 533

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVG
Sbjct: 534  HLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 593

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            KQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 594  KQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  538 bits (1386), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 290/622 (46%), Positives = 402/622 (64%), Gaps = 31/622 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1   MEQNQQSTAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQHDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N +
Sbjct: 120 TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLDHYDQVEAGNYRLADLITGFVDPNIA 179

Query: 206 SNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------------- 245
                      N +E    E  SA+ + +  ++   E                       
Sbjct: 180 EEETA------NIDEHFADEDESAESAVDVDDESDEEDESDSSSSSDDSDSDNSIDPEVA 233

Query: 246 --KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 303
             +F+ +     K      K G + +        +++     R   K  + L  +++N I
Sbjct: 234 RERFAALREQHTKTLATIAKHGRSGKRAKDQIAQLADIFKQFRLVPKQFDVLVLSMKNMI 293

Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 363
            +V   E+Q+ +++V+  GMP+  F  +   N  N  WV    K    +   L +    I
Sbjct: 294 KRVRAEERQLQKVLVDIAGMPKDEFEALIVANGSNDTWVAKALKSTKAWAKRLPKYEERI 353

Query: 364 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 423
           +     L N++    L +  +R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+R
Sbjct: 354 RLSLDNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNR 413

Query: 424 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483
           GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 414 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 473

Query: 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543
           ETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DS
Sbjct: 474 ETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDS 533

Query: 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 603
           HLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVG
Sbjct: 534 HLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 593

Query: 604 KQFDVTRERIRQIEAKALRKLR 625
           KQFDVTRERIRQIEAKALRKLR
Sbjct: 594 KQFDVTRERIRQIEAKALRKLR 615


>gi|121591668|ref|ZP_01678905.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
 gi|121546475|gb|EAX56696.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 2740-80]
          Length = 603

 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 309/608 (50%), Positives = 405/608 (66%), Gaps = 34/608 (5%)

Query: 848  FSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATE 905
            ++E+ND LP +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  
Sbjct: 2    YAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAA 61

Query: 906  AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTI 965
            AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI
Sbjct: 62   AALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTI 121

Query: 966  MEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ 1025
              IL   D++   E+++ +++ G +D N           +      I  E S ADL+ E 
Sbjct: 122  PYILEQFDRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADED 174

Query: 1026 LEKLKYESLI-------------------------KFSNISFHFDKMRKAFEKEGYNSES 1060
               ++ E                            KF+ +   F  ++ A  + G +S  
Sbjct: 175  DAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQ 234

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +A + + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI 
Sbjct: 235  ASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIA 294

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+
Sbjct: 295  LFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRR 354

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 355  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 414

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 415  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 474

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  
Sbjct: 475  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 534

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 535  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 594

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 595  EVLRSFLD 602



 Score =  538 bits (1387), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 302/595 (50%), Positives = 396/595 (66%), Gaps = 34/595 (5%)

Query: 58  FSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATE 115
           ++E+ND LP +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  
Sbjct: 2   YAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAA 61

Query: 116 AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTI 175
           AALS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI
Sbjct: 62  AALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTI 121

Query: 176 MEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQ 235
             IL   D++   E+++ +++ G +D N           +      I  E S ADL+ E 
Sbjct: 122 PYILEQFDRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADED 174

Query: 236 LEKLKYESLI-------------------------KFSNISFHFDKMRKAFEKEGYNSES 270
              ++ E                            KF+ +   F  ++ A  + G +S  
Sbjct: 175 DAVVEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQ 234

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +A + + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI 
Sbjct: 235 ASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIA 294

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+
Sbjct: 295 LFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRR 354

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 355 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 414

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 415 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 474

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  
Sbjct: 475 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 534

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 535 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 589


>gi|119504971|ref|ZP_01627048.1| putative transcriptional regulator, Fis family protein [marine gamma
            proteobacterium HTCC2080]
 gi|119459257|gb|EAW40355.1| putative transcriptional regulator, Fis family protein [marine gamma
            proteobacterium HTCC2080]
          Length = 606

 Score =  553 bits (1424), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 294/602 (48%), Positives = 403/602 (66%), Gaps = 11/602 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  GKE+GYLT++E+ND LP+DI + + +E II+    M I V E   D + L+L
Sbjct: 10   RLKALIAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELIL 69

Query: 892  S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            +  + ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70   TEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKGNKN 1006
            G+++++ A++  P    ++  A D ++K E K+ +I+ G +D      S+          
Sbjct: 130  GIRELMAAMAHYPGVARKLSNAYDMVAKEERKLSDILIGYLDPAEHVPSAQEMAEAAEAA 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066
                    + +  +   + +E  K     +F+ +     K  KA    GY  ++     +
Sbjct: 190  AATATDDDDDTEVETGPDPVEAKK-----RFTALKRQCTKTEKAIATHGYGHKTATAEMD 244

Query: 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 1126
             +       + T +  + L D  R  +  + + E+ I+ I V +C M R  FIK F  +E
Sbjct: 245  KLGELFKFFKLTPRVFDPLIDEPRESLYIIRKQERAIMRIAVRECRMDRKEFIKSFSGSE 304

Query: 1127 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 1186
             +  W+    + + D    L  +   I+ +Q+++  ++    L + ++++INR+M  GE 
Sbjct: 305  SDSRWISRVAR-KKDIGARLALHKDDIQRMQRRISEVEQATGLSVAEIKEINRRMSMGEA 363

Query: 1187 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246
            +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 364  RARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 423

Query: 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306
            ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMP
Sbjct: 424  ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMP 483

Query: 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 1366
            E+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    +    +D+L  
Sbjct: 484  EDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTISSPVDSATEEGLTEATQDVLAG 543

Query: 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP+R   L+ F
Sbjct: 544  LTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYLRSF 603

Query: 1427 LE 1428
            L+
Sbjct: 604  LD 605



 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 291/597 (48%), Positives = 398/597 (66%), Gaps = 12/597 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  GKE+GYLT++E+ND LP+DI + + +E II+    M I V E   D + L+L
Sbjct: 10  RLKALIAKGKEQGYLTYAEVNDHLPQDISEPDQVEDIIQMINDMGIQVFEQAPDADELIL 69

Query: 102 S--NITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           +  + ++D+       AAL+ V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEE
Sbjct: 70  TEGDRSADEIAAAEAAAALAAVENEAGRTTDPVRMYMREMGTVELLTREGEIVIAKRIEE 129

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN---FSSNNRVIKGNKN 216
           G+++++ A++  P    ++  A D ++K E K+ +I+ G +D      S+          
Sbjct: 130 GIRELMAAMAHYPGVARKLSNAYDMVAKEERKLSDILIGYLDPAEHVPSAQEMAEAAEAA 189

Query: 217 NNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 276
                   + +  +   + +E  K     +F+ +     K  KA    GY  ++     +
Sbjct: 190 AATATDDDDDTEVETGPDPVEAKK-----RFTALKRQCTKTEKAIATHGYGHKTATAEMD 244

Query: 277 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENE 336
            +       + T +  + L D  R  +  + + E+ I+ I V +C M R  FIK F  +E
Sbjct: 245 KLGELFKFFKLTPRVFDPLIDEPRESLYIIRKQERAIMRIAVRECRMDRKEFIKSFSGSE 304

Query: 337 INLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEM 396
            +  W+    + + D    L  +   I+ +Q+++  ++    L + ++++INR+M  GE 
Sbjct: 305 SDSRWISRVAR-KKDIGARLALHKDDIQRMQRRISEVEQATGLSVAEIKEINRRMSMGEA 363

Query: 397 KARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456
           +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
Sbjct: 364 RARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 423

Query: 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 516
           ATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +  +MEMP
Sbjct: 424 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMP 483

Query: 517 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS 576
           E+K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED  + +P D+A    +    +D+L  
Sbjct: 484 EDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDVTISSPVDSATEEGLTEATQDVLAG 543

Query: 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           LT RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR P   D+L
Sbjct: 544 LTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSDYL 600


>gi|400288721|ref|ZP_10790753.1| sigma-70 factor (RpoD) [Psychrobacter sp. PAMC 21119]
          Length = 639

 Score =  552 bits (1423), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 298/626 (47%), Positives = 416/626 (66%), Gaps = 29/626 (4%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +   LI++GKE+GYLT++E+ND LP+ I + + IE I++    + I + E   D + +++
Sbjct: 12   QLATLIQMGKEQGYLTYAEVNDQLPDSITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 892  SNITSDDDVEEATEAALSTVD-SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            ++ +SDD+      AA+     +D GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72   NDDSSDDESAADEAAAVLAAVETDPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------------- 993
            ++D+ HA+S  P T+  +L    K+   + K+ +++ G +D                   
Sbjct: 132  IRDVQHAMSYWPGTVQFVLDEYQKVQDGDKKLSDVITGFLDPETEEDKIAAQEAKEAAKE 191

Query: 994  -------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL----KYESLIKFSNISF 1042
                      N  VIK   N  E+    +S   D + E+ E+       E  ++   I  
Sbjct: 192  ERERIKEEKENPPVIKPKANAKEDLDDDDSDDIDDAEEEEEETGGIDPEEVRLRLEEIEN 251

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             F K ++A    G  S    +A+  ++   + ++   +  +++   + +  + V + E+Q
Sbjct: 252  LFIKAKQALLDYGRGSVQADEAYAQLAERFMMLKLNNRLSDQVMAIMHDVYDDVRKQERQ 311

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            I+ +V+ +  MPR  F K FP NE N++W+    K +  +   L +    +  LQ+K+ +
Sbjct: 312  IMRLVIRRGRMPRDEFRKTFPSNETNVDWLIERIKGKPAFAGTLEKVTDDVILLQRKIRD 371

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
             +  + + ++D++D+ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 372  YEQQLDMKIHDMKDVARRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 431

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+
Sbjct: 432  EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRV 491

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 492  SRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDG 551

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
             + +P D A +A +R   +D+L +LT RE++VL+MRFGI+M +DHTLEEVGKQFDVTRER
Sbjct: 552  TISSPVDDATSAGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRER 611

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFLE 1428
            IRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 612  IRQIEAKALRKLRHPSRSEHLRSFLE 637



 Score =  536 bits (1381), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 290/613 (47%), Positives = 407/613 (66%), Gaps = 29/613 (4%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +   LI++GKE+GYLT++E+ND LP+ I + + IE I++    + I + E   D + +++
Sbjct: 12  QLATLIQMGKEQGYLTYAEVNDQLPDSITESDQIEDIVQMLTDVGIKIFESAPDADDILM 71

Query: 102 SNITSDDDVEEATEAALSTVD-SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           ++ +SDD+      AA+     +D GRT DP++MYMREMG+V+LLTR+GEI IAKRIEEG
Sbjct: 72  NDDSSDDESAADEAAAVLAAVETDPGRTTDPVRMYMREMGTVDLLTREGEIVIAKRIEEG 131

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN----------------- 203
           ++D+ HA+S  P T+  +L    K+   + K+ +++ G +D                   
Sbjct: 132 IRDVQHAMSYWPGTVQFVLDEYQKVQDGDKKLSDVITGFLDPETEEDKIAAQEAKEAAKE 191

Query: 204 -------FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL----KYESLIKFSNISF 252
                     N  VIK   N  E+    +S   D + E+ E+       E  ++   I  
Sbjct: 192 ERERIKEEKENPPVIKPKANAKEDLDDDDSDDIDDAEEEEEETGGIDPEEVRLRLEEIEN 251

Query: 253 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            F K ++A    G  S    +A+  ++   + ++   +  +++   + +  + V + E+Q
Sbjct: 252 LFIKAKQALLDYGRGSVQADEAYAQLAERFMMLKLNNRLSDQVMAIMHDVYDDVRKQERQ 311

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
           I+ +V+ +  MPR  F K FP NE N++W+    K +  +   L +    +  LQ+K+ +
Sbjct: 312 IMRLVIRRGRMPRDEFRKTFPSNETNVDWLIERIKGKPAFAGTLEKVTDDVILLQRKIRD 371

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
            +  + + ++D++D+ R+M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 372 YEQQLDMKIHDMKDVARRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 431

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+
Sbjct: 432 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRV 491

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED 
Sbjct: 492 SRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDG 551

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
            + +P D A +A +R   +D+L +LT RE++VL+MRFGI+M +DHTLEEVGKQFDVTRER
Sbjct: 552 TISSPVDDATSAGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRER 611

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 612 IRQIEAKALRKLR 624


>gi|78486147|ref|YP_392072.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
 gi|78364433|gb|ABB42398.1| sigma 70 (RpoD) [Thiomicrospira crunogena XCL-2]
          Length = 594

 Score =  552 bits (1423), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 297/597 (49%), Positives = 401/597 (67%), Gaps = 19/597 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 894
            LI+  K+ GYLTFS++ND LP+DI + + +  ++   R   I + E   D + L+     
Sbjct: 13   LIERAKDLGYLTFSDVNDVLPDDI-EEDQLGQVLTILRDFGIQLFESAPDADELLTKEGE 71

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            T DD   EA   AL+ VD++FGRT DP++MYMREMGSVELLTR GE+EIAKRIE G++DM
Sbjct: 72   TFDDAAAEAAILALAEVDAEFGRTTDPVRMYMREMGSVELLTRQGEVEIAKRIEYGIRDM 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNNEEK 1011
            + A++  P   ME+L +  +I   E K  +++ G I   D        +   N +   ++
Sbjct: 132  LEAMAKYPQVAMELLASFSRIEDGEGKTADLIQGFIRPADLVDIPIEELSPDNDSGEPKE 191

Query: 1012 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 1071
              I     D   ++L KL  ++L              KA EK GY+    +K    I   
Sbjct: 192  DGINPEELDAFLQKLAKLNADTL--------------KAEEKNGYSDPKSVKKRAEIVAL 237

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
            +  ++ +   + ++   ++ +++ + + E+ ++  V+ + G+PR  F+K+F  +E + + 
Sbjct: 238  LATVKLSPVFVNRMIKGIKLRVSSIREQERNVVNAVMRQVGVPRPSFLKLFVGSETDYDV 297

Query: 1132 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 1191
            +D   +   D    L      +K  Q++L  ++    +P+N  + I + +   E  AR A
Sbjct: 298  LDRLKEAHPDKADALEEVRADVKRAQKRLAMIEKAEKMPINQYKTIYKDLSKAESIARIA 357

Query: 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251
            KREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV+KFEYRRGYKFSTYATWWI
Sbjct: 358  KREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWI 417

Query: 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 1311
            RQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEMPE+K+R
Sbjct: 418  RQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEMPEDKVR 477

Query: 1312 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
            K+MKIAKEP+SME+PVGDDEDS LGDFIED N+L+P D+A    M   V+++L++LTPRE
Sbjct: 478  KVMKIAKEPISMETPVGDDEDSSLGDFIEDSNILSPQDSADLEGMGETVREMLSTLTPRE 537

Query: 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            +KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +LK FL+
Sbjct: 538  AKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAERLKSFLD 594



 Score =  535 bits (1378), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 289/584 (49%), Positives = 391/584 (66%), Gaps = 19/584 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 104
           LI+  K+ GYLTFS++ND LP+DI + + +  ++   R   I + E   D + L+     
Sbjct: 13  LIERAKDLGYLTFSDVNDVLPDDI-EEDQLGQVLTILRDFGIQLFESAPDADELLTKEGE 71

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           T DD   EA   AL+ VD++FGRT DP++MYMREMGSVELLTR GE+EIAKRIE G++DM
Sbjct: 72  TFDDAAAEAAILALAEVDAEFGRTTDPVRMYMREMGSVELLTRQGEVEIAKRIEYGIRDM 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLI---DKNFSSNNRVIKGNKNNNEEK 221
           + A++  P   ME+L +  +I   E K  +++ G I   D        +   N +   ++
Sbjct: 132 LEAMAKYPQVAMELLASFSRIEDGEGKTADLIQGFIRPADLVDIPIEELSPDNDSGEPKE 191

Query: 222 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 281
             I     D   ++L KL  ++L              KA EK GY+    +K    I   
Sbjct: 192 DGINPEELDAFLQKLAKLNADTL--------------KAEEKNGYSDPKSVKKRAEIVAL 237

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           +  ++ +   + ++   ++ +++ + + E+ ++  V+ + G+PR  F+K+F  +E + + 
Sbjct: 238 LATVKLSPVFVNRMIKGIKLRVSSIREQERNVVNAVMRQVGVPRPSFLKLFVGSETDYDV 297

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
           +D   +   D    L      +K  Q++L  ++    +P+N  + I + +   E  AR A
Sbjct: 298 LDRLKEAHPDKADALEEVRADVKRAQKRLAMIEKAEKMPINQYKTIYKDLSKAESIARIA 357

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           KREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAV+KFEYRRGYKFSTYATWWI
Sbjct: 358 KREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWI 417

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEMPE+K+R
Sbjct: 418 RQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEMPEDKVR 477

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           K+MKIAKEP+SME+PVGDDEDS LGDFIED N+L+P D+A    M   V+++L++LTPRE
Sbjct: 478 KVMKIAKEPISMETPVGDDEDSSLGDFIEDSNILSPQDSADLEGMGETVREMLSTLTPRE 537

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 538 AKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 581


>gi|145633515|ref|ZP_01789244.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
 gi|144985884|gb|EDJ92492.1| aspartate ammonia-lyase [Haemophilus influenzae 3655]
          Length = 628

 Score =  552 bits (1422), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 305/633 (48%), Positives = 414/633 (65%), Gaps = 28/633 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 993
            TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------KFSNI 1040
               +N + +   + +E++   E  S++   E  E                     KF  +
Sbjct: 180  IEEHNGLDEDFSDEDEDEDDEEEGSSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQL 239

Query: 1041 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQ 1095
                 K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +
Sbjct: 240  REQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKR 294

Query: 1096 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 1155
            V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E
Sbjct: 295  VRYEERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVTKALKSSKPWAKRLIKYEDRIYE 354

Query: 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 1215
                L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 355  ALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGL 414

Query: 1216 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275
            QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 415  QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 474

Query: 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335
            INK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 475  INKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHL 534

Query: 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395
            GDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 535  GDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQ 594

Query: 1396 FDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            FDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  FDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 627



 Score =  537 bits (1383), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 298/620 (48%), Positives = 405/620 (65%), Gaps = 28/620 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 203
           TR+ EI IAKRIEEG+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI-------------KFSNI 250
              +N + +   + +E++   E  S++   E  E                     KF  +
Sbjct: 180 IEEHNGLDEDFSDEDEDEDDEEEGSSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQL 239

Query: 251 SFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQ 305
                K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +
Sbjct: 240 REQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKR 294

Query: 306 VTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE 365
           V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E
Sbjct: 295 VRYEERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVTKALKSSKPWAKRLIKYEDRIYE 354

Query: 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL 425
               L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGL
Sbjct: 355 ALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGL 414

Query: 426 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 485
           QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET
Sbjct: 415 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 474

Query: 486 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545
           INK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHL
Sbjct: 475 INKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHL 534

Query: 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605
           GDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQ
Sbjct: 535 GDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQ 594

Query: 606 FDVTRERIRQIEAKALRKLR 625
           FDVTRERIRQIEAKALRKLR
Sbjct: 595 FDVTRERIRQIEAKALRKLR 614


>gi|408821898|ref|ZP_11206788.1| RNA polymerase sigma factor RpoD [Pseudomonas geniculata N1]
          Length = 617

 Score =  552 bits (1422), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 304/608 (50%), Positives = 400/608 (65%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLTDEEPAPPAAAADD 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            + +     +    D      E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190  SADADAEGDEDEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248  LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308  SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
             +L+ FL+
Sbjct: 608  EQLRSFLD 615



 Score =  536 bits (1381), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 390/595 (65%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLTDEEPAPPAAAADD 189

Query: 217 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           + +     +    D      E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190 SADADAEGDEDEDDDVDGGDEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248 LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308 SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|262376664|ref|ZP_06069892.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
 gi|262308374|gb|EEY89509.1| RNA polymerase sigma factor rpoD [Acinetobacter lwoffii SH145]
 gi|407007501|gb|EKE23136.1| hypothetical protein ACD_6C00584G0005 [uncultured bacterium]
          Length = 628

 Score =  552 bits (1422), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 293/618 (47%), Positives = 402/618 (65%), Gaps = 30/618 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  GKE+GYLTF+E+ND LP+ I + E IE II+    + I V +   +++  M  +  
Sbjct: 14   LISRGKEQGYLTFAEVNDHLPDSITESEQIEDIIQMLNDVGIPVHDRAPESDDTMFEDTA 73

Query: 896  SDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
               D     EAA    +V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74   EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++H+I+  P  +  +L         E ++ +++ G +D             +   EE +L
Sbjct: 134  VLHSIAYWPNAVEVVLQEYKDYEAGERRLADLLSGYLDPESDEEI-----PEVLEEEAVL 188

Query: 1014 IESSSADLSTEQLEKLKYE----------------------SLIKFSNISFHFDKMRKAF 1051
             E  +    + +  KL  +                      +  +F+ +   +   +   
Sbjct: 189  AEDETDSKKSTKDVKLDDDEEEEEADSDDESEADSGPDPEIAKARFTELENAWLNTKATI 248

Query: 1052 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 1111
            EK G +S+   +A   ++   +  +FT +  + + + +R   +Q+   E++++   V + 
Sbjct: 249  EKHGRDSKQAEEALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRG 308

Query: 1112 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             M R  F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L 
Sbjct: 309  RMDRTQFRTSFPGQESNPAWLDEQIAKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLD 368

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            +  ++DI ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 369  VKGIKDIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 428

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 429  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 488

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 489  GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPIDA 548

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
            A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 549  ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR   L+ FLE
Sbjct: 609  LRKLRHPSRSEHLRSFLE 626



 Score =  536 bits (1380), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 285/605 (47%), Positives = 393/605 (64%), Gaps = 30/605 (4%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  GKE+GYLTF+E+ND LP+ I + E IE II+    + I V +   +++  M  +  
Sbjct: 14  LISRGKEQGYLTFAEVNDHLPDSITESEQIEDIIQMLNDVGIPVHDRAPESDDTMFEDTA 73

Query: 106 SDDDVEEATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
              D     EAA    +V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRIEEG++D
Sbjct: 74  EAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEISIAKRIEEGIRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++H+I+  P  +  +L         E ++ +++ G +D             +   EE +L
Sbjct: 134 VLHSIAYWPNAVEVVLQEYKDYEAGERRLADLLSGYLDPESDEEI-----PEVLEEEAVL 188

Query: 224 IESSSADLSTEQLEKLKYE----------------------SLIKFSNISFHFDKMRKAF 261
            E  +    + +  KL  +                      +  +F+ +   +   +   
Sbjct: 189 AEDETDSKKSTKDVKLDDDEEEEEADSDDESEADSGPDPEIAKARFTELENAWLNTKATI 248

Query: 262 EKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
           EK G +S+   +A   ++   +  +FT +  + + + +R   +Q+   E++++   V + 
Sbjct: 249 EKHGRDSKQAEEALQALATVFMMFKFTPRLFDIISEMIRGTHDQIRGAEREVMRYAVRRG 308

Query: 322 GMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            M R  F   FP  E N  W+D +  K   D    L +  P +   QQK+ +++ ++ L 
Sbjct: 309 RMDRTQFRTSFPGQESNPAWLDEQIAKTPADQKAYLEKVRPDVLAFQQKIADIEKELGLD 368

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +  ++DI ++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 369 VKGIKDIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 428

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R+SRQ+LQE 
Sbjct: 429 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINRVSRQLLQEM 488

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED N+ +P DA
Sbjct: 489 GREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNITSPIDA 548

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRERIRQIEAKA
Sbjct: 549 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 621 LRKLR 625
           LRKLR
Sbjct: 609 LRKLR 613


>gi|344209014|ref|YP_004794155.1| RNA polymerase sigma-70 subunit RpoD [Stenotrophomonas maltophilia
            JV3]
 gi|343780376|gb|AEM52929.1| RNA polymerase, sigma 70 subunit, RpoD [Stenotrophomonas maltophilia
            JV3]
          Length = 617

 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 304/608 (50%), Positives = 401/608 (65%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLADEEPAPPAAAADD 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +++     +    D      E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190  SSDADAEGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248  LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308  SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
             +L+ FL+
Sbjct: 608  EQLRSFLD 615



 Score =  536 bits (1380), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 391/595 (65%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D              +
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLADEEPAPPAAAADD 189

Query: 217 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +++     +    D      E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190 SSDADAEGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248 LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308 SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|386720113|ref|YP_006186439.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia D457]
 gi|384079675|emb|CCH14277.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia D457]
          Length = 617

 Score =  551 bits (1421), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 306/608 (50%), Positives = 404/608 (66%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKG 1003
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G   L D+  +        
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLADEEPAPPAVAADD 189

Query: 1004 NKNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            + + + E    E    +   E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190  SSDADAEGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248  LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308  SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
             +L+ FL+
Sbjct: 608  EQLRSFLD 615



 Score =  535 bits (1379), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 299/595 (50%), Positives = 394/595 (66%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG---LIDKNFSSNNRVIKG 213
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G   L D+  +        
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLTDYEAHKEGKKRLAEVIVGFNDLADEEPAPPAVAADD 189

Query: 214 NKNNNEEKILIESSSADLSTEQLEKL---KYESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           + + + E    E    +   E+         E   +   +S  F+  +KA  K   + ++
Sbjct: 190 SSDADAEGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFNAFKKAATK--GDKKN 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248 LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMASIKAHERRVLNLATVTARMPRKDFIR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308 SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|244539374|dbj|BAH83417.1| RNA polymerase sigma factor [Candidatus Ishikawaella capsulata
            Mpkobe]
          Length = 619

 Score =  551 bits (1419), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/605 (49%), Positives = 410/605 (67%), Gaps = 12/605 (1%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K+L+  GKE+GYLT++++ND LP DI   E IE II+    M I + E   DT+ L+L
Sbjct: 8    QLKLLVTRGKEQGYLTYADLNDHLPNDISHSEQIEDIIQMIHDMGIPIVEKTPDTDDLIL 67

Query: 892  S-NI-TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            + NI +S +D+ +     L  V  + G T D ++MYMREMGSVELLTRDGEI+IAKRIE+
Sbjct: 68   NENIHSSYEDIVQVAAQVLCEVQYEIGTTTDTVRMYMREMGSVELLTRDGEIDIAKRIED 127

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 1009
            G+  +  +++  P  I+ +L   DKI   E+++ +++   +D N       I  +  + +
Sbjct: 128  GINQIQSSVAEYPKAIIYLLDQYDKIDSGELRLSDLISSFVDPNAKIEPTFIPDHIVSRK 187

Query: 1010 EKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
              I ++    D   E  +      L   KF  +   F+   +  + +G      ++    
Sbjct: 188  INIDLDDDEEDHDHEDDDNTIDPELAREKFLLLRKQFELTARVIKNKGREHIDALQEIKK 247

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            +S+     R  +K    L + +R+ +N++ + E+ I+++ V +   P+  FI +F  NE 
Sbjct: 248  LSDIFKQFRLVSKQFSYLVNNMRHIMNRIRRQERIIMKLYVEQYKFPKKKFIAMFTGNET 307

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIK----ELQQKLINLQTDIVLPLNDLRDINRKMIA 1183
            N++ + +   I+H  N    +NI  ++    +  Q+LI ++ +  L +  ++DINR+M  
Sbjct: 308  NIDLLKS-ILIKHKNN---YQNIEEMEKHLMQCLQQLIVIEQETGLKIEQIKDINRRMAI 363

Query: 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 1243
            GE K R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 364  GEAKTRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 423

Query: 1244 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 1303
            STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR ILQETG EP P  ++  M
Sbjct: 424  STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRHILQETGHEPTPEELSEHM 483

Query: 1304 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 1363
             +PEEKIRK++KIAKEP+SME+P+GDDEDSH+GDF+ED  +  P D+A + S+R+  +++
Sbjct: 484  LIPEEKIRKVLKIAKEPISMETPLGDDEDSHIGDFLEDNTIKLPLDSATSDSLRTATQNV 543

Query: 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423
            L  LT RE+KVLRMRFGI+MS+DHTLEEVGKQF+VTRERIRQIEAKALRKLRHPSR   L
Sbjct: 544  LTGLTAREAKVLRMRFGIDMSTDHTLEEVGKQFNVTRERIRQIEAKALRKLRHPSRSEVL 603

Query: 1424 KIFLE 1428
            + FLE
Sbjct: 604  RSFLE 608



 Score =  536 bits (1381), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 297/615 (48%), Positives = 410/615 (66%), Gaps = 13/615 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K+L+  GKE+GYLT++++ND LP DI   E IE II+    M I + E   DT+ L+L
Sbjct: 8   QLKLLVTRGKEQGYLTYADLNDHLPNDISHSEQIEDIIQMIHDMGIPIVEKTPDTDDLIL 67

Query: 102 S-NI-TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           + NI +S +D+ +     L  V  + G T D ++MYMREMGSVELLTRDGEI+IAKRIE+
Sbjct: 68  NENIHSSYEDIVQVAAQVLCEVQYEIGTTTDTVRMYMREMGSVELLTRDGEIDIAKRIED 127

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNE 219
           G+  +  +++  P  I+ +L   DKI   E+++ +++   +D N       I  +  + +
Sbjct: 128 GINQIQSSVAEYPKAIIYLLDQYDKIDSGELRLSDLISSFVDPNAKIEPTFIPDHIVSRK 187

Query: 220 EKILIESSSADLSTEQLEKLKYESLI--KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
             I ++    D   E  +      L   KF  +   F+   +  + +G      ++    
Sbjct: 188 INIDLDDDEEDHDHEDDDNTIDPELAREKFLLLRKQFELTARVIKNKGREHIDALQEIKK 247

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           +S+     R  +K    L + +R+ +N++ + E+ I+++ V +   P+  FI +F  NE 
Sbjct: 248 LSDIFKQFRLVSKQFSYLVNNMRHIMNRIRRQERIIMKLYVEQYKFPKKKFIAMFTGNET 307

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIK----ELQQKLINLQTDIVLPLNDLRDINRKMIA 393
           N++ + +   I+H  N    +NI  ++    +  Q+LI ++ +  L +  ++DINR+M  
Sbjct: 308 NIDLLKS-ILIKHKNN---YQNIEEMEKHLMQCLQQLIVIEQETGLKIEQIKDINRRMAI 363

Query: 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 453
           GE K R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF
Sbjct: 364 GEAKTRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 423

Query: 454 STYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKM 513
           STYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR ILQETG EP P  ++  M
Sbjct: 424 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRHILQETGHEPTPEELSEHM 483

Query: 514 EMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDI 573
            +PEEKIRK++KIAKEP+SME+P+GDDEDSH+GDF+ED  +  P D+A + S+R+  +++
Sbjct: 484 LIPEEKIRKVLKIAKEPISMETPLGDDEDSHIGDFLEDNTIKLPLDSATSDSLRTATQNV 543

Query: 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR-PLAHDWL 632
           L  LT RE+KVLRMRFGI+MS+DHTLEEVGKQF+VTRERIRQIEAKALRKLR P   + L
Sbjct: 544 LTGLTAREAKVLRMRFGIDMSTDHTLEEVGKQFNVTRERIRQIEAKALRKLRHPSRSEVL 603

Query: 633 EQRTHQNEKIIACSS 647
                ++EK I   S
Sbjct: 604 RSFLEEHEKSIDIKS 618


>gi|358011069|ref|ZP_09142879.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp.
            P8-3-8]
          Length = 629

 Score =  550 bits (1417), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 297/627 (47%), Positives = 421/627 (67%), Gaps = 25/627 (3%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            E+ +   +   LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   
Sbjct: 3    EMHSPTSQVAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAP 62

Query: 885  DTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
            +++  M   ++  +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63   ESDDTMFEGNSEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIS 122

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIEEG++D++H+I+  P  +  +L         E ++ +I+ G +D    S+  + +
Sbjct: 123  IAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYETGERRLADILSGYLDPE--SDEVIPE 180

Query: 1003 GNKNNNEEKILIESSSADLSTE-QLEKLKYE-------------------SLIKFSNISF 1042
              +   EE    ES+SA  + + +L+    E                   +  +F  ++ 
Sbjct: 181  VIEEETEELEDDESASAKPTKDVKLDDDDEEEESEGDDDSEGESGPDPEIAKARFDELAS 240

Query: 1043 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
             ++  ++   K G NS+   +A  +++   +  +FT +  + + + +R    Q+   E++
Sbjct: 241  VWNNAKETLAKHGRNSDEGKEAIESLAAVFMMFKFTPRLFDIISEMIRGTHEQIRTSERE 300

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLI 1161
            ++   V +  M R  F   FP  E N  W+D +  K   +    L +  P +   QQ++ 
Sbjct: 301  VMRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQIAKAPAESKAYLEKVRPDVLAFQQQIA 360

Query: 1162 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 1221
            +++ ++ L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 361  DIEKELNLNVKEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 420

Query: 1222 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 1281
            QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R
Sbjct: 421  QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINR 480

Query: 1282 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341
            +SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 481  VSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIED 540

Query: 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401
             N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRE
Sbjct: 541  GNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRE 600

Query: 1402 RIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RIRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 601  RIRQIEAKALRKLRHPSRSEHLRSFLE 627



 Score =  534 bits (1375), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 289/614 (47%), Positives = 412/614 (67%), Gaps = 25/614 (4%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           E+ +   +   LI  GKE+GYLT++E+ND LP+ I + E IE II+  + + I V E   
Sbjct: 3   EMHSPTSQVAALISRGKEQGYLTYAEVNDHLPDSITESEQIEDIIQMLQDVGIPVHERAP 62

Query: 95  DTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
           +++  M   ++  +D+  EE   A L++V+++ GRT DP++MYMREMG+VELLTR+GEI 
Sbjct: 63  ESDDTMFEGNSEAADEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVELLTREGEIS 122

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIEEG++D++H+I+  P  +  +L         E ++ +I+ G +D    S+  + +
Sbjct: 123 IAKRIEEGIRDVLHSIAYWPNAVEVVLQEYKDYETGERRLADILSGYLDPE--SDEVIPE 180

Query: 213 GNKNNNEEKILIESSSADLSTE-QLEKLKYE-------------------SLIKFSNISF 252
             +   EE    ES+SA  + + +L+    E                   +  +F  ++ 
Sbjct: 181 VIEEETEELEDDESASAKPTKDVKLDDDDEEEESEGDDDSEGESGPDPEIAKARFDELAS 240

Query: 253 HFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
            ++  ++   K G NS+   +A  +++   +  +FT +  + + + +R    Q+   E++
Sbjct: 241 VWNNAKETLAKHGRNSDEGKEAIESLAAVFMMFKFTPRLFDIISEMIRGTHEQIRTSERE 300

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKELQQKLI 371
           ++   V +  M R  F   FP  E N  W+D +  K   +    L +  P +   QQ++ 
Sbjct: 301 VMRYAVRRGRMDRTQFRTSFPGQESNPAWLDEQIAKAPAESKAYLEKVRPDVLAFQQQIA 360

Query: 372 NLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLI 431
           +++ ++ L + +++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLI
Sbjct: 361 DIEKELNLNVKEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 420

Query: 432 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISR 491
           QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI+R
Sbjct: 421 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKINR 480

Query: 492 ISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551
           +SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLGDFIED
Sbjct: 481 VSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLGDFIED 540

Query: 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611
            N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQFDVTRE
Sbjct: 541 GNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRE 600

Query: 612 RIRQIEAKALRKLR 625
           RIRQIEAKALRKLR
Sbjct: 601 RIRQIEAKALRKLR 614


>gi|254522302|ref|ZP_05134357.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
 gi|219719893|gb|EED38418.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
          Length = 617

 Score =  550 bits (1417), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 304/608 (50%), Positives = 401/608 (65%), Gaps = 13/608 (2%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10   EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 892  -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                  N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70   NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D    +         +
Sbjct: 130  IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLTDEAPAPAAAAADD 189

Query: 1007 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 1060
            +++     +    D      E+         E   +   +S  F   +KA  K   + ++
Sbjct: 190  SDDADADGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFTAFKKAATK--GDKKN 247

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248  LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMADIKSHERRVLNLATVTARMPRKDFIR 307

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
             +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308  SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368  MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488  KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 548  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 1421 YKLKIFLE 1428
             +L+ FL+
Sbjct: 608  EQLRSFLD 615



 Score =  534 bits (1375), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 297/595 (49%), Positives = 391/595 (65%), Gaps = 13/595 (2%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           + K LI  G E+GYLT++E+ND LP+D++D E IE II     M I V E   D ETL+L
Sbjct: 10  EIKQLISKGLEQGYLTYAEVNDHLPDDMVDPEQIEDIIGMINGMGIDVHEVAPDVETLLL 69

Query: 102 -----SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                 N   DD   E   AALS +D++ GRT DP++MYMREMG+VELLTR+GEI IAKR
Sbjct: 70  NDGNTGNREVDDTAAEEAAAALSALDTEGGRTTDPVRMYMREMGTVELLTREGEIAIAKR 129

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IEEGL  +  A+   P ++  +L   +   + + ++ E++ G  D    +         +
Sbjct: 130 IEEGLSQVQAALGQFPVSVESLLNDYEAHKEGKKRLAEVIVGFNDLTDEAPAPAAAAADD 189

Query: 217 NNEEKILIESSSADLSTEQLEKLK------YESLIKFSNISFHFDKMRKAFEKEGYNSES 270
           +++     +    D      E+         E   +   +S  F   +KA  K   + ++
Sbjct: 190 SDDADADGDEDEDDDVEGGEEEAAPTGPDPEEVAARMQALSDAFTAFKKAATK--GDKKN 247

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +    +S   + ++      + L   LR+ +  +   E+++L +      MPR  FI+
Sbjct: 248 LPRLREEMSAVFVTLKLPLPLTDVLTKQLRDTMADIKSHERRVLNLATVTARMPRKDFIR 307

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
            +  N+ NL WV++  K +  ++  L      I   QQ  I+++    L L +L++I+R 
Sbjct: 308 SWEGNQTNLEWVEDALKRKQKWSSALREVKDQIIAEQQATIDIEKLTQLDLEELKEISRA 367

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KARKAK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 368 MAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 427

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQ+ G E  P  +A
Sbjct: 428 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQQYGREATPEELA 487

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK+MKIAKEP+SME+P+GDDEDSHLGDFIED N+ +P +   N ++   V
Sbjct: 488 KEMDMPEDKIRKVMKIAKEPISMETPIGDDEDSHLGDFIEDTNVESPIENTTNINLSETV 547

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 548 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|343519915|ref|ZP_08756889.1| RNA polymerase sigma factor RpoD [Haemophilus pittmaniae HK 85]
 gi|343392214|gb|EGV04785.1| RNA polymerase sigma factor RpoD [Haemophilus pittmaniae HK 85]
          Length = 627

 Score =  550 bits (1416), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 303/636 (47%), Positives = 419/636 (65%), Gaps = 35/636 (5%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED+ID E  + +++T +    
Sbjct: 1    MEQNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF- 994
            TR+ EI IAKRIEEG+ ++  AI++ P  +  +L     + +   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQGAIAAYPEALNPLLAHYADVEEGNYRLADLITGFVDPNII 179

Query: 995  -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI------------KFSNIS 1041
               N  V   + +++E    I + S +   E  E    +               KF  + 
Sbjct: 180  EEENADVQYAHSDDDENAETINAESDEEEDESDENSSSDDSESDNSIDPELAREKFYELK 239

Query: 1042 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQV 1096
                K  +A EK G + +   +A   I+  +LG      R   K  ++L   ++N I QV
Sbjct: 240  AQHSKTLQAIEKHGRHGK---RAKEQIA--LLGEIFKQFRLVPKQFDQLVFAMKNMIKQV 294

Query: 1097 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 1156
               E+Q+ +++V+  GMP+  F  +   +  N  W++   K    +     + +P  +E 
Sbjct: 295  RAEERQLQKVLVDIAGMPKDEFESLVLSHSSNPTWLEKALKSTKSW----AKRLPKYEER 350

Query: 1157 QQKLIN----LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
             +  I+    L+    L + ++R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351  LRLSIDNLALLEQRSNLSVLEIREICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471  IETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531  SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 591  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 626



 Score =  535 bits (1378), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 296/623 (47%), Positives = 410/623 (65%), Gaps = 35/623 (5%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED+ID E  + +++T +    
Sbjct: 1   MEQNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDVIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF- 204
           TR+ EI IAKRIEEG+ ++  AI++ P  +  +L     + +   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQGAIAAYPEALNPLLAHYADVEEGNYRLADLITGFVDPNII 179

Query: 205 -SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI------------KFSNIS 251
              N  V   + +++E    I + S +   E  E    +               KF  + 
Sbjct: 180 EEENADVQYAHSDDDENAETINAESDEEEDESDENSSSDDSESDNSIDPELAREKFYELK 239

Query: 252 FHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQV 306
               K  +A EK G + +   +A   I+  +LG      R   K  ++L   ++N I QV
Sbjct: 240 AQHSKTLQAIEKHGRHGK---RAKEQIA--LLGEIFKQFRLVPKQFDQLVFAMKNMIKQV 294

Query: 307 TQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKEL 366
              E+Q+ +++V+  GMP+  F  +   +  N  W++   K    +     + +P  +E 
Sbjct: 295 RAEERQLQKVLVDIAGMPKDEFESLVLSHSSNPTWLEKALKSTKSW----AKRLPKYEER 350

Query: 367 QQKLIN----LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
            +  I+    L+    L + ++R+I   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 351 LRLSIDNLALLEQRSNLSVLEIREICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 410

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 411 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 470

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 471 IETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 530

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 531 SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 590

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 591 GKQFDVTRERIRQIEAKALRKLR 613


>gi|419801431|ref|ZP_14326658.1| RNA polymerase sigma factor RpoD [Haemophilus parainfluenzae HK262]
 gi|419846311|ref|ZP_14369564.1| RNA polymerase sigma factor RpoD [Haemophilus parainfluenzae HK2019]
 gi|385193645|gb|EIF41002.1| RNA polymerase sigma factor RpoD [Haemophilus parainfluenzae HK262]
 gi|386414051|gb|EIJ28620.1| RNA polymerase sigma factor RpoD [Haemophilus parainfluenzae HK2019]
          Length = 629

 Score =  550 bits (1416), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 299/646 (46%), Positives = 414/646 (64%), Gaps = 53/646 (8%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1    MEQNQQSSAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQHDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLNNYDQVEAGNYRLADLITGFVDPN-- 177

Query: 996  SNNRVIKGNKNNNEEKILIESSSA---------------------------------DLS 1022
                V++    N +E    E  S                                  +++
Sbjct: 178  ----VVEEEAANVDEHFTDEDESTQSVADVDDESDEEDEGDSSSSSDDSDSDNSIDPEVA 233

Query: 1023 TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSI 1082
             E+   L+ +     + I+ H         + G  ++  I    +I  +    R   K  
Sbjct: 234  RERFAALREQHTKTLATIAKHG--------RSGKRAKDQIAQLADIFKQ---FRLVPKQF 282

Query: 1083 EKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY 1142
            + L  +++N I +V   E+Q+ +++V+  GMP+  F  +   N  N  WV    K    +
Sbjct: 283  DVLVLSMKNMIKRVRVEERQLQKVLVDIAGMPKDEFEALIIANGSNDAWVAKALKSTKAW 342

Query: 1143 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 1202
               L +    I+     L N++    L +  +R+I   +  GE KAR+AK+EM EANLRL
Sbjct: 343  AKRLPKYEERIRLSLDNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRL 402

Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
            VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 403  VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 462

Query: 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 1322
            ARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+S
Sbjct: 463  ARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPIS 522

Query: 1323 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 1382
            ME+P+GDD+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+
Sbjct: 523  METPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGID 582

Query: 1383 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 583  MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  535 bits (1377), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 292/633 (46%), Positives = 405/633 (63%), Gaps = 53/633 (8%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLT++EIND LPED+ID E  + +++T ++   
Sbjct: 1   MEQNQQSSAEQYSEQIEQLMELGRTQGYLTYAEINDLLPEDVIDPEYYDKLLQTLQHDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +ML++   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDEMMLNDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIEEG+ ++  AI++ P  + E+L   D++     ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEEGIDEVQTAIAAYPEALTELLNNYDQVEAGNYRLADLITGFVDPN-- 177

Query: 206 SNNRVIKGNKNNNEEKILIESSSA---------------------------------DLS 232
               V++    N +E    E  S                                  +++
Sbjct: 178 ----VVEEEAANVDEHFTDEDESTQSVADVDDESDEEDEGDSSSSSDDSDSDNSIDPEVA 233

Query: 233 TEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSI 292
            E+   L+ +     + I+ H         + G  ++  I    +I  +    R   K  
Sbjct: 234 RERFAALREQHTKTLATIAKHG--------RSGKRAKDQIAQLADIFKQ---FRLVPKQF 282

Query: 293 EKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY 352
           + L  +++N I +V   E+Q+ +++V+  GMP+  F  +   N  N  WV    K    +
Sbjct: 283 DVLVLSMKNMIKRVRVEERQLQKVLVDIAGMPKDEFEALIIANGSNDAWVAKALKSTKAW 342

Query: 353 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 412
              L +    I+     L N++    L +  +R+I   +  GE KAR+AK+EM EANLRL
Sbjct: 343 AKRLPKYEERIRLSLDNLANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRL 402

Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
           VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 403 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 462

Query: 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 532
           ARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+S
Sbjct: 463 ARTIRIPVHMIETINKLNRISRQMLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPIS 522

Query: 533 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 592
           ME+P+GDD+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+
Sbjct: 523 METPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGID 582

Query: 593 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 583 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 615


>gi|68249130|ref|YP_248242.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
 gi|68057329|gb|AAX87582.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae 86-028NP]
          Length = 623

 Score =  549 bits (1414), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 302/628 (48%), Positives = 411/628 (65%), Gaps = 23/628 (3%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 993
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFD 1045
               +N + +   + ++E+    +   D  +E                   KF  +     
Sbjct: 180  IEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHS 239

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIE 1100
            K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E
Sbjct: 240  KTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE 294

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            +Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L
Sbjct: 295  RQLQKILVDIAGMPKDDFEKIITANGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL 354

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
               + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 355  AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 414

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 415  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 474

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 475  RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 534

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 535  DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 594

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  ERIRQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  534 bits (1375), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 295/615 (47%), Positives = 402/615 (65%), Gaps = 23/615 (3%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 203
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFD 255
              +N + +   + ++E+    +   D  +E                   KF  +     
Sbjct: 180 IEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHS 239

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIE 310
           K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E
Sbjct: 240 KTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE 294

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           +Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L
Sbjct: 295 RQLQKILVDIAGMPKDDFEKIITANGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL 354

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
              + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 355 AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 414

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 415 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 474

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 475 RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 534

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 535 DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 594

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 595 ERIRQIEAKALRKLR 609


>gi|145628917|ref|ZP_01784717.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145635386|ref|ZP_01791088.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
 gi|144979387|gb|EDJ89073.1| DNA primase [Haemophilus influenzae 22.1-21]
 gi|145267392|gb|EDK07394.1| aspartate ammonia-lyase [Haemophilus influenzae PittAA]
          Length = 623

 Score =  548 bits (1413), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 302/628 (48%), Positives = 411/628 (65%), Gaps = 23/628 (3%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 993
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFD 1045
               +N + +   + ++E+    +   D  +E                   KF  +     
Sbjct: 180  IEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHS 239

Query: 1046 KMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIE 1100
            K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E
Sbjct: 240  KTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE 294

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
            +Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L
Sbjct: 295  RQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL 354

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
               + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 355  AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 414

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 415  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 474

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 475  RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 534

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 535  DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 594

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  ERIRQIEAKALRKLRHPSRSETLRSFLD 622



 Score =  533 bits (1374), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 295/615 (47%), Positives = 402/615 (65%), Gaps = 23/615 (3%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN-- 203
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N  
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFD 255
              +N + +   + ++E+    +   D  +E                   KF  +     
Sbjct: 180 IEEHNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHS 239

Query: 256 KMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIE 310
           K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E
Sbjct: 240 KTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQE 294

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
           +Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L
Sbjct: 295 RQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNL 354

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
              + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 355 AITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL 414

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++
Sbjct: 415 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 474

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIE
Sbjct: 475 RISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIE 534

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTR
Sbjct: 535 DSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 594

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKLR
Sbjct: 595 ERIRQIEAKALRKLR 609


>gi|148825193|ref|YP_001289946.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
 gi|148715353|gb|ABQ97563.1| aspartate ammonia-lyase [Haemophilus influenzae PittEE]
          Length = 645

 Score =  548 bits (1411), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 302/625 (48%), Positives = 409/625 (65%), Gaps = 23/625 (3%)

Query: 821  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 879
            N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 26   NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 85

Query: 880  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
             +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 86   LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 144

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSS 996
             EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N     
Sbjct: 145  DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAEIEE 204

Query: 997  NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMR 1048
            +N + +   + ++E+    +   D  +E                   KF  +     K  
Sbjct: 205  HNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHSKTL 264

Query: 1049 KAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIEKQI 1103
               EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E+Q+
Sbjct: 265  AVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQL 319

Query: 1104 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 1163
             +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L   
Sbjct: 320  QKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNLAIT 379

Query: 1164 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 1223
            + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380  EENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 1224 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 1283
            GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440  GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 499

Query: 1284 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 1343
            RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 500  RQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 559

Query: 1344 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560  LELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 1404 RQIEAKALRKLRHPSRYYKLKIFLE 1428
            RQIEAKALRKLRHPSR   L+ FL+
Sbjct: 620  RQIEAKALRKLRHPSRSETLRSFLD 644



 Score =  533 bits (1373), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 295/612 (48%), Positives = 400/612 (65%), Gaps = 23/612 (3%)

Query: 31  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 89
           N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 26  NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 85

Query: 90  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
            +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 86  LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 144

Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKN--FSS 206
            EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G +D N     
Sbjct: 145 DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAEIEE 204

Query: 207 NNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI--------KFSNISFHFDKMR 258
           +N + +   + ++E+    +   D  +E                   KF  +     K  
Sbjct: 205 HNGLDEDFSDEDDEEESSNADVEDNESESTSDSSDSDNSIDPEVAREKFQQLREQHSKTL 264

Query: 259 KAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQIEKQI 313
              EK G + +   +A + I+  +LG      R   K  + L  +++  + +V   E+Q+
Sbjct: 265 AVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRYQERQL 319

Query: 314 LEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINL 373
            +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E    L   
Sbjct: 320 QKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALNNLAIT 379

Query: 374 QTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQE 433
           + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQE
Sbjct: 380 EENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 439

Query: 434 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRIS 493
           GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RIS
Sbjct: 440 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS 499

Query: 494 RQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553
           RQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDFIED  
Sbjct: 500 RQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDST 559

Query: 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERI
Sbjct: 560 LELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 619

Query: 614 RQIEAKALRKLR 625
           RQIEAKALRKLR
Sbjct: 620 RQIEAKALRKLR 631


>gi|212212053|ref|YP_002302989.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212010463|gb|ACJ17844.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
          Length = 698

 Score =  546 bits (1408), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 298/610 (48%), Positives = 397/610 (65%), Gaps = 16/610 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94   ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154  DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210  KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 1061
              + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269  ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329  LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 1122 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389  FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446  RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566  LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 626  ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 685

Query: 1419 RYYKLKIFLE 1428
            R  KL  F+E
Sbjct: 686  RAEKLHSFIE 695



 Score =  530 bits (1366), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 290/597 (48%), Positives = 388/597 (64%), Gaps = 16/597 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94  ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154 DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210 KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 271
             + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269 ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329 LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 332 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389 FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446 RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566 LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 626 ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 682


>gi|29654887|ref|NP_820579.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161831165|ref|YP_001597431.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
 gi|81628631|sp|Q83BB6.1|RPOD_COXBU RecName: Full=RNA polymerase sigma factor RpoD
 gi|29542156|gb|AAO91093.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|161763032|gb|ABX78674.1| RNA polymerase sigma factor RpoD [Coxiella burnetii RSA 331]
          Length = 698

 Score =  546 bits (1407), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 298/610 (48%), Positives = 397/610 (65%), Gaps = 16/610 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94   ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154  DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210  KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 1061
              + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269  ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329  LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 1122 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389  FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446  RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566  LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 626  ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 685

Query: 1419 RYYKLKIFLE 1428
            R  KL  F+E
Sbjct: 686  RAEKLHSFIE 695



 Score =  530 bits (1366), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 290/597 (48%), Positives = 388/597 (64%), Gaps = 16/597 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94  ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154 DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210 KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 271
             + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269 ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329 LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 332 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389 FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446 RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566 LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 626 ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 682


>gi|154705741|ref|YP_001423814.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355027|gb|ABS76489.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 698

 Score =  546 bits (1407), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 298/610 (48%), Positives = 397/610 (65%), Gaps = 16/610 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94   ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154  DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210  KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 1061
              + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269  ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329  LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 1122 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389  FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446  RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566  LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 626  ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 685

Query: 1419 RYYKLKIFLE 1428
            R  KL  F+E
Sbjct: 686  RAEKLHSFIE 695



 Score =  530 bits (1366), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 290/597 (48%), Positives = 388/597 (64%), Gaps = 16/597 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94  ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154 DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210 KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 271
             + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269 ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329 LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 332 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389 FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446 RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +M+MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566 LGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 626 ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 682


>gi|410447666|ref|ZP_11301758.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86E]
 gi|409979246|gb|EKO36008.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86E]
          Length = 601

 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 291/595 (48%), Positives = 402/595 (67%), Gaps = 10/595 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI+ G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D +TLMLS  +
Sbjct: 14   LIEKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADTLMLSESS 73

Query: 896  SDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
             D D    E    AL+ V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D
Sbjct: 74   DDQDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRD 133

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 1013
            ++ A    P  +  I+   +++   + K+ E++ G +++       V      + + K L
Sbjct: 134  LLDASVHYPGIVEHIIDFYEQVKSEDKKLSELLTGFLEEM----EEVPSAGPGSEKAKQL 189

Query: 1014 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
             ES     +   L +++     + +N+   F+K  K  E +G +S+        +     
Sbjct: 190  EESDEEVDNGPDLAEVQR----RMTNLKRQFNKTHKVVESKGRHSKEAKAEFAKLGLIFQ 245

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
             ++F+ K  E L    R+ + ++   EK+I  + V    +PR  FI ++ +N   + WVD
Sbjct: 246  FLKFSPKMFEDLAFFARSDLAEIRLHEKRIQFLFVKSARIPRKDFIAMYKDNITKVKWVD 305

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
            +    +      L    P +   Q+ +  ++  + L + D+++INR M  GE K R+AK+
Sbjct: 306  SLMTNKKYSKKSLEHIKPDVVIAQKAIKGVEERVGLSIKDIKEINRAMSMGETKMRRAKK 365

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            +M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 366  DMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 425

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK+
Sbjct: 426  AITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKV 485

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDDEDS+LGDFIED  + +P   A   S+     D+L+SLT RE+K
Sbjct: 486  LKIAKEPISMETPIGDDEDSNLGDFIEDTVIHSPLKNATEGSLHFATDDVLSSLTAREAK 545

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK FL+
Sbjct: 546  VLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSSHLKNFLD 600



 Score =  530 bits (1365), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 283/582 (48%), Positives = 393/582 (67%), Gaps = 10/582 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI+ G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D +TLMLS  +
Sbjct: 14  LIEKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADTLMLSESS 73

Query: 106 SDDD--VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
            D D    E    AL+ V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D
Sbjct: 74  DDQDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRD 133

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKIL 223
           ++ A    P  +  I+   +++   + K+ E++ G +++       V      + + K L
Sbjct: 134 LLDASVHYPGIVEHIIDFYEQVKSEDKKLSELLTGFLEEM----EEVPSAGPGSEKAKQL 189

Query: 224 IESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
            ES     +   L +++     + +N+   F+K  K  E +G +S+        +     
Sbjct: 190 EESDEEVDNGPDLAEVQR----RMTNLKRQFNKTHKVVESKGRHSKEAKAEFAKLGLIFQ 245

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
            ++F+ K  E L    R+ + ++   EK+I  + V    +PR  FI ++ +N   + WVD
Sbjct: 246 FLKFSPKMFEDLAFFARSDLAEIRLHEKRIQFLFVKSARIPRKDFIAMYKDNITKVKWVD 305

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
           +    +      L    P +   Q+ +  ++  + L + D+++INR M  GE K R+AK+
Sbjct: 306 SLMTNKKYSKKSLEHIKPDVVIAQKAIKGVEERVGLSIKDIKEINRAMSMGETKMRRAKK 365

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           +M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 366 DMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 425

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK+
Sbjct: 426 AITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKV 485

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           +KIAKEP+SME+P+GDDEDS+LGDFIED  + +P   A   S+     D+L+SLT RE+K
Sbjct: 486 LKIAKEPISMETPIGDDEDSNLGDFIEDTVIHSPLKNATEGSLHFATDDVLSSLTAREAK 545

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 546 VLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 587


>gi|153208748|ref|ZP_01946986.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat Q177']
 gi|212219307|ref|YP_002306094.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120575780|gb|EAX32404.1| RNA polymerase sigma factor RpoD [Coxiella burnetii 'MSU Goat Q177']
 gi|212013569|gb|ACJ20949.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 698

 Score =  544 bits (1402), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 297/610 (48%), Positives = 397/610 (65%), Gaps = 16/610 (2%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 886
            E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94   ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 887  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154  DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210  KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 1005 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 1061
              + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269  ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 1062 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 1121
            +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329  LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 1122 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 1178
            FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389  FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 1238
            R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446  RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 1239 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 1298
            RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506  RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 1299 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 1358
            +  +++MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566  LGRRIDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418
              ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS
Sbjct: 626  ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 685

Query: 1419 RYYKLKIFLE 1428
            R  KL  F+E
Sbjct: 686  RAEKLHSFIE 695



 Score =  528 bits (1361), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 289/597 (48%), Positives = 388/597 (64%), Gaps = 16/597 (2%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDT 96
           E+ R  F  L++  K +GYL   ++ + LP D  D   +E II     M I V E   D 
Sbjct: 94  ESQRLGFGALLEEAKNKGYLVHEDLINLLPNDYADPSQMEGIIGRLTEMGIKVFEIPPDA 153

Query: 97  ETLMLSNITS--DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++L+L   T   DD++ E     L+T      RT DP++MYMREMGSVELLTR+GEI IA
Sbjct: 154 DSLLLEEDTQSDDDEINEDVAEVLATET----RTTDPVRMYMREMGSVELLTREGEIVIA 209

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIEEG++ ++ A+   P  I + +   D I   E ++ +++ G  D+  S+ + V    
Sbjct: 210 KRIEEGIRQVMGAVVQYPELIEKFIKEYDTIVATEGRLSDLLIGFFDEEESTASPVAP-E 268

Query: 215 KNNNEEKILIESSSADLSTEQLEKLKYESLIK---FSNISFHFDKMRKAFEKEGYNSESY 271
             + E +   E    +  +++  +   + LI       +   + + + A ++ G  + + 
Sbjct: 269 ARDKEAETSDEDDGGEGGSDEFGESGPDPLITQQHMEELKKLYGRYQNAIKRYGKKAPAT 328

Query: 272 IKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKV 331
           +K    ++      + + K   +L   LR  +      E+ I+   V K   PR  FI  
Sbjct: 329 LKHQKALAELFSTFKLSIKQFNRLTGQLRRMLRAARAQERLIMSYCVVKAKTPRKKFIAS 388

Query: 332 FPENEINLNWVD---NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDIN 388
           FP NE N+ W++   NE K Q      L +    I   Q+ L  L+    L + ++++IN
Sbjct: 389 FPHNETNMKWLEQYKNENKEQAKR---LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEIN 445

Query: 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYR 448
           R++  GE K+R+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYR
Sbjct: 446 RRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 505

Query: 449 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508
           RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQILQETG E  P  
Sbjct: 506 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEE 565

Query: 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRS 568
           +  +++MPEEK+RK++KIAKEP+SME+P+G+DEDS+LGDFIED NM +P D A +A +  
Sbjct: 566 LGRRIDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLME 625

Query: 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
             ++IL++LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 626 ATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 682


>gi|424863602|ref|ZP_18287514.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86A]
 gi|400756923|gb|EJP71135.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86A]
          Length = 604

 Score =  544 bits (1401), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 287/599 (47%), Positives = 399/599 (66%), Gaps = 15/599 (2%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI+ G+E+GYLT+S++ND LP+DI D + ++ II     + + V E   D +TLML+   
Sbjct: 14   LIEKGREQGYLTYSDVNDHLPDDISDPDQVDEIIGMINDLGLQVHETAPDADTLMLAESE 73

Query: 896  SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
              DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D+
Sbjct: 74   DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRDL 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK-----NFSSNNRVIKGNKNNNE 1009
            ++A    P T+  +L     +   E KI++ + G +++     +    ++  K      E
Sbjct: 134  LNASVMYPKTVEYVLHYFQLVKDGEKKINDFLTGFLEEMEEVPSAGPGSQRAKEEAEAAE 193

Query: 1010 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 1069
                  SS  D+   Q          + +++   F+K  K  +K+G +S+        + 
Sbjct: 194  SSDEEGSSGPDMKEVQK---------RMTSLKRQFNKTTKVIDKKGRHSKEANAEFKKLG 244

Query: 1070 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 1129
                 ++F+ +  E +    R+ +N + + EK I   +V    +PR  F+ ++PEN   +
Sbjct: 245  EIFQFLKFSPRMFEDIAAIARHGLNSIREKEKFIQTQLVKNARIPRKDFLVLYPENLTKV 304

Query: 1130 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 1189
             WVD   K +     +L +    +   Q+ ++ ++  + L + ++++INR M  GE K R
Sbjct: 305  RWVDGLMKEKKYKKDLLEKVKQDVVIAQKDILEIENKVGLSIKEIKEINRNMSMGETKMR 364

Query: 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249
            +AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 365  RAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 424

Query: 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 1309
            WIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K
Sbjct: 425  WIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDK 484

Query: 1310 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 1369
            +RK++KIAKEP+S E+P+GDDEDS LGDFIED  + +P + A   S+     D+L SLT 
Sbjct: 485  VRKVLKIAKEPISTETPIGDDEDSSLGDFIEDTVIESPLENATEESLHFATDDVLASLTA 544

Query: 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK FL+
Sbjct: 545  REAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSSHLKSFLD 603



 Score =  528 bits (1360), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 279/586 (47%), Positives = 390/586 (66%), Gaps = 15/586 (2%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI+ G+E+GYLT+S++ND LP+DI D + ++ II     + + V E   D +TLML+   
Sbjct: 14  LIEKGREQGYLTYSDVNDHLPDDISDPDQVDEIIGMINDLGLQVHETAPDADTLMLAESE 73

Query: 106 SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
             DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D+
Sbjct: 74  DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRDL 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDK-----NFSSNNRVIKGNKNNNE 219
           ++A    P T+  +L     +   E KI++ + G +++     +    ++  K      E
Sbjct: 134 LNASVMYPKTVEYVLHYFQLVKDGEKKINDFLTGFLEEMEEVPSAGPGSQRAKEEAEAAE 193

Query: 220 EKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNIS 279
                 SS  D+   Q          + +++   F+K  K  +K+G +S+        + 
Sbjct: 194 SSDEEGSSGPDMKEVQK---------RMTSLKRQFNKTTKVIDKKGRHSKEANAEFKKLG 244

Query: 280 NEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 339
                ++F+ +  E +    R+ +N + + EK I   +V    +PR  F+ ++PEN   +
Sbjct: 245 EIFQFLKFSPRMFEDIAAIARHGLNSIREKEKFIQTQLVKNARIPRKDFLVLYPENLTKV 304

Query: 340 NWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKAR 399
            WVD   K +     +L +    +   Q+ ++ ++  + L + ++++INR M  GE K R
Sbjct: 305 RWVDGLMKEKKYKKDLLEKVKQDVVIAQKDILEIENKVGLSIKEIKEINRNMSMGETKMR 364

Query: 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459
           +AK++M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW
Sbjct: 365 RAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 424

Query: 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519
           WIRQAITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K
Sbjct: 425 WIRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDK 484

Query: 520 IRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTP 579
           +RK++KIAKEP+S E+P+GDDEDS LGDFIED  + +P + A   S+     D+L SLT 
Sbjct: 485 VRKVLKIAKEPISTETPIGDDEDSSLGDFIEDTVIESPLENATEESLHFATDDVLASLTA 544

Query: 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RE+KVLRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 545 REAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 590


>gi|323144090|ref|ZP_08078731.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
 gi|322416132|gb|EFY06825.1| RNA polymerase sigma factor RpoD [Succinatimonas hippei YIT 12066]
          Length = 648

 Score =  543 bits (1399), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 306/646 (47%), Positives = 416/646 (64%), Gaps = 55/646 (8%)

Query: 832  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891
            +FK LI  GKE+GYLT  EIND +P DII  + +   I+TF  M I+V E   D + ++L
Sbjct: 9    EFKQLIARGKEQGYLTIEEINDLIPPDIISGDQLSVFIQTFIDMGINVCETPPDPDDILL 68

Query: 892  SNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
            S+ +  +++DVE       STVD   GRT DP++MYMREMG+V LLTR  EIEI+KRIE 
Sbjct: 69   SDSSQAAEEDVETVANQLDSTVD--IGRTTDPVRMYMREMGNVSLLTRKDEIEISKRIER 126

Query: 950  GLKDMIHAISSCPTTIMEILIAADKI--SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            G  D+   I   P  + E+    D+     +EI++ +IV G  + +    N  I  +   
Sbjct: 127  GTNDVQMCIVEYPLAMEELFRRYDEALAPDSEIRLGDIVVGFSEPSKEEINIDIDDSVET 186

Query: 1008 NE--EKILIESSSADLSTEQLEKLKYESLI------------------------------ 1035
             E  EK++ E  SA++   QL+ +K E+                                
Sbjct: 187  EEDIEKLIDEEESAEV---QLDDVKEENTGKAKKGKKSKVEDDPDSDEDEDEDSASQADS 243

Query: 1036 ---------KFSNISFHFDKMRKAFEKEGYNS-ESYIKAHNNISNEMLGIRFTAKSIEKL 1085
                     KF+ +   ++K+  A  K+G  + + Y +    +S      R   + ++ L
Sbjct: 244  GPDPELVKQKFTELRIQYEKVVAAHAKKGSAAVKKYKQELQKLSEMFSTFRLVPQVLDSL 303

Query: 1086 CDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF---PENEINLNWVDNETKIQHDY 1142
               + + +++V   + +I E+ VN CGM +L  +K F    E+E +++W D   K +  Y
Sbjct: 304  LRKMHDMMDRVKNQDHRIREVAVNICGM-KLDELKAFYTDSEHESDMSWFDKALKSKRPY 362

Query: 1143 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 1202
               L    P I+E    L  ++T+  + +  LRD++R+++ G+  A+KAK+EM EANLRL
Sbjct: 363  VARLKDYRPVIEECVNALKEVETESGISIARLRDLSRRVMMGDAMAKKAKKEMVEANLRL 422

Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
            VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 423  VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 482

Query: 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 1322
            ARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A KM +PE+KIRK+MKIAKEP+S
Sbjct: 483  ARTIRIPVHMIETINKLNRISRQMLQEKGREPTPEELAEKMGLPEDKIRKVMKIAKEPIS 542

Query: 1323 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 1382
            +E+PVGDD+DSHLGDFIED +++ P++AA + S+++ + ++L+ + PRE++VLRMRFGI 
Sbjct: 543  LETPVGDDDDSHLGDFIEDSSIVVPAEAATSESLKNAINNVLDEMPPREAQVLRMRFGIG 602

Query: 1383 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            M SDHTLEEVG+QF VTRERIRQIEAKALRKLRHP R   L+ FL+
Sbjct: 603  MPSDHTLEEVGRQFGVTRERIRQIEAKALRKLRHPCRSAGLRGFLD 648



 Score =  530 bits (1364), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 300/633 (47%), Positives = 408/633 (64%), Gaps = 55/633 (8%)

Query: 42  KFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101
           +FK LI  GKE+GYLT  EIND +P DII  + +   I+TF  M I+V E   D + ++L
Sbjct: 9   EFKQLIARGKEQGYLTIEEINDLIPPDIISGDQLSVFIQTFIDMGINVCETPPDPDDILL 68

Query: 102 SNIT--SDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
           S+ +  +++DVE       STVD   GRT DP++MYMREMG+V LLTR  EIEI+KRIE 
Sbjct: 69  SDSSQAAEEDVETVANQLDSTVD--IGRTTDPVRMYMREMGNVSLLTRKDEIEISKRIER 126

Query: 160 GLKDMIHAISSCPTTIMEILIAADKI--SKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           G  D+   I   P  + E+    D+     +EI++ +IV G  + +    N  I  +   
Sbjct: 127 GTNDVQMCIVEYPLAMEELFRRYDEALAPDSEIRLGDIVVGFSEPSKEEINIDIDDSVET 186

Query: 218 NE--EKILIESSSADLSTEQLEKLKYESLI------------------------------ 245
            E  EK++ E  SA++   QL+ +K E+                                
Sbjct: 187 EEDIEKLIDEEESAEV---QLDDVKEENTGKAKKGKKSKVEDDPDSDEDEDEDSASQADS 243

Query: 246 ---------KFSNISFHFDKMRKAFEKEGYNS-ESYIKAHNNISNEMLGIRFTAKSIEKL 295
                    KF+ +   ++K+  A  K+G  + + Y +    +S      R   + ++ L
Sbjct: 244 GPDPELVKQKFTELRIQYEKVVAAHAKKGSAAVKKYKQELQKLSEMFSTFRLVPQVLDSL 303

Query: 296 CDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVF---PENEINLNWVDNETKIQHDY 352
              + + +++V   + +I E+ VN CGM +L  +K F    E+E +++W D   K +  Y
Sbjct: 304 LRKMHDMMDRVKNQDHRIREVAVNICGM-KLDELKAFYTDSEHESDMSWFDKALKSKRPY 362

Query: 353 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 412
              L    P I+E    L  ++T+  + +  LRD++R+++ G+  A+KAK+EM EANLRL
Sbjct: 363 VARLKDYRPVIEECVNALKEVETESGISIARLRDLSRRVMMGDAMAKKAKKEMVEANLRL 422

Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
           VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 423 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 482

Query: 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 532
           ARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A KM +PE+KIRK+MKIAKEP+S
Sbjct: 483 ARTIRIPVHMIETINKLNRISRQMLQEKGREPTPEELAEKMGLPEDKIRKVMKIAKEPIS 542

Query: 533 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 592
           +E+PVGDD+DSHLGDFIED +++ P++AA + S+++ + ++L+ + PRE++VLRMRFGI 
Sbjct: 543 LETPVGDDDDSHLGDFIEDSSIVVPAEAATSESLKNAINNVLDEMPPREAQVLRMRFGIG 602

Query: 593 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           M SDHTLEEVG+QF VTRERIRQIEAKALRKLR
Sbjct: 603 MPSDHTLEEVGRQFGVTRERIRQIEAKALRKLR 635


>gi|295698783|ref|YP_003603438.1| RNA polymerase sigma factor RpoD, partial [Candidatus Riesia
           pediculicola USDA]
 gi|291157386|gb|ADD79831.1| RNA polymerase sigma factor RpoD, partial [Candidatus Riesia
           pediculicola USDA]
          Length = 607

 Score =  543 bits (1398), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 407/614 (66%), Gaps = 43/614 (7%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+T   M I V+E V D +
Sbjct: 4   NPKSQLKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDED 63

Query: 98  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
            L+L++ TS  D EE  EAA   LS+V+ + GRT DPI+MYMREMG++ELLTR+GEI+IA
Sbjct: 64  ELILTDPTSSTD-EETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIA 122

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL-----------IDKN 203
           KRIE+G+  +  +IS  P +I  IL         E+K+ +I+ GL           +DKN
Sbjct: 123 KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDIITGLSSEDTFSSSKNVDKN 182

Query: 204 FSSN-----NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE----SLIKFSNISFHF 254
           FSS      N V+    +NN EK  I  S     T   ++  +     +  KF  +   +
Sbjct: 183 FSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDPKIARKKFLELQNQY 242

Query: 255 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
           +K+  + ++ G  S   I    ++       R   K ++ L   +R  I ++   EK I+
Sbjct: 243 EKVTHSLKENGIKSSQSILDIQDLCEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLII 302

Query: 315 EIVVNKCGMPRLHFIKVFPEN--EINLNWV--------DNETKIQHDYNLILCRNIPSIK 364
            I   +  +P+ +F+ +F EN  E +L  +         +E K + D  ++   N     
Sbjct: 303 NISFKEYKIPKKYFLNLFSENPKEYDLKELIVSNRYNKKDEKKFKLDSTIVQALN----- 357

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
               +L  ++ D  + ++ +++I RK+  GE  AR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 358 ----ELNEIEKDTGISISKIKEIGRKISIGETIARRAKKEMVEANLRLVISIAKKYTNRG 413

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 414 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 473

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++ ISRQILQETG EP P  ++ +M +PEEKIRK++KIA+EP+SME+P+GDDEDSH
Sbjct: 474 TINKLNHISRQILQETGREPSPEELSERMLIPEEKIRKVLKIAREPISMETPIGDDEDSH 533

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED  +  P ++A + S+RS   ++L+ LT RE+KVLRMRFGI+M +DHTLEEVGK
Sbjct: 534 LGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGK 593

Query: 605 QFDVTRERIRQIEA 618
           QFDVTRERIRQIEA
Sbjct: 594 QFDVTRERIRQIEA 607



 Score =  543 bits (1398), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 305/614 (49%), Positives = 407/614 (66%), Gaps = 43/614 (7%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            N + + K+L+  GKE+GYLT+SE+ND LPEDI+D + IE II+T   M I V+E V D +
Sbjct: 4    NPKSQLKVLVNKGKEKGYLTYSEVNDNLPEDIVDSDQIEDIIQTIIDMGIRVTEEVPDED 63

Query: 888  TLMLSNITSDDDVEEATEAA---LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
             L+L++ TS  D EE  EAA   LS+V+ + GRT DPI+MYMREMG++ELLTR+GEI+IA
Sbjct: 64   ELILTDPTSSTD-EETVEAATQVLSSVEQEIGRTTDPIRMYMREMGTIELLTREGEIDIA 122

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL-----------IDKN 993
            KRIE+G+  +  +IS  P +I  IL         E+K+ +I+ GL           +DKN
Sbjct: 123  KRIEDGINQIQRSISEYPKSISYILKQYFLFESGEMKLSDIITGLSSEDTFSSSKNVDKN 182

Query: 994  FSSN-----NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE----SLIKFSNISFHF 1044
            FSS      N V+    +NN EK  I  S     T   ++  +     +  KF  +   +
Sbjct: 183  FSSMKLNRINSVLDEILSNNYEKKDISKSQNSTRTNVEDEWNHIDPKIARKKFLELQNQY 242

Query: 1045 DKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
            +K+  + ++ G  S   I    ++       R   K ++ L   +R  I ++   EK I+
Sbjct: 243  EKVTHSLKENGIKSSQSILDIQDLCEIFKQFRLVPKQLDFLISDIRKTIEKIKIQEKLII 302

Query: 1105 EIVVNKCGMPRLHFIKVFPEN--EINLNWV--------DNETKIQHDYNLILCRNIPSIK 1154
             I   +  +P+ +F+ +F EN  E +L  +         +E K + D  ++   N     
Sbjct: 303  NISFKEYKIPKKYFLNLFSENPKEYDLKELIVSNRYNKKDEKKFKLDSTIVQALN----- 357

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
                +L  ++ D  + ++ +++I RK+  GE  AR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 358  ----ELNEIEKDTGISISKIKEIGRKISIGETIARRAKKEMVEANLRLVISIAKKYTNRG 413

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 414  LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 473

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++ ISRQILQETG EP P  ++ +M +PEEKIRK++KIA+EP+SME+P+GDDEDSH
Sbjct: 474  TINKLNHISRQILQETGREPSPEELSERMLIPEEKIRKVLKIAREPISMETPIGDDEDSH 533

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED  +  P ++A + S+RS   ++L+ LT RE+KVLRMRFGI+M +DHTLEEVGK
Sbjct: 534  LGDFIEDTTLELPLESATSESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGK 593

Query: 1395 QFDVTRERIRQIEA 1408
            QFDVTRERIRQIEA
Sbjct: 594  QFDVTRERIRQIEA 607


>gi|262164053|ref|ZP_06031792.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
 gi|262027581|gb|EEY46247.1| RNA polymerase sigma factor RpoD [Vibrio mimicus VM223]
          Length = 595

 Score =  543 bits (1398), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 306/601 (50%), Positives = 398/601 (66%), Gaps = 34/601 (5%)

Query: 855  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATEAALSTVD 912
            +P +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  AALS+V+
Sbjct: 1    MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 913  SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 972
            S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  A++  P TI  IL   
Sbjct: 61   SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAVAEYPGTIPYILEQF 120

Query: 973  DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            DK+   E+++ +++ G +D N           +      I  E S ADL+ E  E    E
Sbjct: 121  DKVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDEIADDE 173

Query: 1033 SLI-------------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                                        KF+ +   F  ++ A  + G +S    +A + 
Sbjct: 174  DEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSNQASEASSL 233

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE 
Sbjct: 234  VLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNES 293

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE K
Sbjct: 294  NEEWLDKVLASDKPYVQKIREQEDDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAK 353

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 354  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 413

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE
Sbjct: 414  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPE 473

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  L
Sbjct: 474  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGL 533

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            TPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL
Sbjct: 534  TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 593

Query: 1428 E 1428
            +
Sbjct: 594  D 594



 Score =  528 bits (1360), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 299/588 (50%), Positives = 389/588 (66%), Gaps = 34/588 (5%)

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATEAALSTVD 122
           +P +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  AALS+V+
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  A++  P TI  IL   
Sbjct: 61  SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAVAEYPGTIPYILEQF 120

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 242
           DK+   E+++ +++ G +D N           +      I  E S ADL+ E  E    E
Sbjct: 121 DKVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDEIADDE 173

Query: 243 SLI-------------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
                                       KF+ +   F  ++ A  + G +S    +A + 
Sbjct: 174 DEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSNQASEASSL 233

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE 
Sbjct: 234 VLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNES 293

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE K
Sbjct: 294 NEEWLDKVLASDKPYVQKIREQEDDIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAK 353

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 354 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 413

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE
Sbjct: 414 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPE 473

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  L
Sbjct: 474 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGL 533

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           TPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 534 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 581


>gi|153214921|ref|ZP_01949704.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262151177|ref|ZP_06028315.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
 gi|421338229|ref|ZP_15788667.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-20A2]
 gi|124114994|gb|EAY33814.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 1587]
 gi|262031008|gb|EEY49634.1| RNA polymerase sigma factor RpoD [Vibrio cholerae INDRE 91/1]
 gi|395945349|gb|EJH56015.1| RNA polymerase sigma factor rpoD [Vibrio cholerae HC-20A2]
          Length = 595

 Score =  542 bits (1397), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 305/601 (50%), Positives = 399/601 (66%), Gaps = 34/601 (5%)

Query: 855  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATEAALSTVD 912
            +P +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  AALS+V+
Sbjct: 1    MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 913  SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 972
            S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  IL   
Sbjct: 61   SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQF 120

Query: 973  DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 1032
            D++   E+++ +++ G +D N           +      I  E S ADL+ E    ++ E
Sbjct: 121  DRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDAVVEDE 173

Query: 1033 SLI-------------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 1067
                                        KF+ +   F  ++ A  + G +S    +A + 
Sbjct: 174  DEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDL 233

Query: 1068 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 1127
            + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE 
Sbjct: 234  VLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNES 293

Query: 1128 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
            N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE K
Sbjct: 294  NEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAK 353

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
            AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 354  ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 413

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE
Sbjct: 414  TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPE 473

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  L
Sbjct: 474  DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGL 533

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            TPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL
Sbjct: 534  TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 593

Query: 1428 E 1428
            +
Sbjct: 594  D 594



 Score =  528 bits (1360), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 298/588 (50%), Positives = 390/588 (66%), Gaps = 34/588 (5%)

Query: 65  LPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS--DDDVEEATEAALSTVD 122
           +P +I+D E +E II+    M I V E   D + L LS+ T+  D+D  EA  AALS+V+
Sbjct: 1   MPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVE 60

Query: 123 SDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAA 182
           S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  IL   
Sbjct: 61  SEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQF 120

Query: 183 DKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE 242
           D++   E+++ +++ G +D N           +      I  E S ADL+ E    ++ E
Sbjct: 121 DRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDAVVEDE 173

Query: 243 SLI-------------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNN 277
                                       KF+ +   F  ++ A  + G +S    +A + 
Sbjct: 174 DEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDL 233

Query: 278 ISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEI 337
           + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE 
Sbjct: 234 VLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNES 293

Query: 338 NLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
           N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE K
Sbjct: 294 NEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAK 353

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
           AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA
Sbjct: 354 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 413

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE
Sbjct: 414 TWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPE 473

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           +KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  L
Sbjct: 474 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGL 533

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           TPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 534 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 581


>gi|146329704|ref|YP_001209965.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
 gi|146233174|gb|ABQ14152.1| RNA polymerase sigma-70 factor [Dichelobacter nodosus VCS1703A]
          Length = 623

 Score =  541 bits (1395), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 282/625 (45%), Positives = 414/625 (66%), Gaps = 34/625 (5%)

Query: 825  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 884
            E +++ +++K L + G+E+G+LT+ EIN+ LPE  ++ E  + +I         ++E+ +
Sbjct: 9    EDDDVHEEYKELFEQGREQGFLTYEEINETLPESAVEGEKFDELIAF-------LNENGI 61

Query: 885  DTETLMLSNITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
            D          +  DD E      LS+ D++ GRT DP++MYMREMG+V+LLTR+GEI I
Sbjct: 62   DVVETPPEEEEAVTDDEESLANNVLSSADAEVGRTTDPVRMYMREMGAVDLLTREGEIAI 121

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 1003
            AKRIE GL  +   ++  P  I  ++   +++   E ++ ++V+G  D  F+        
Sbjct: 122  AKRIESGLDLVQQTLAEFPLAIAALVAEFERVEAGEGRLSDLVNGYGDP-FAQKTEEATD 180

Query: 1004 --------NKNNNEEKILIE-----------SSSADLST-EQLEKLKYESLIKFSNISFH 1043
                    +  + ++++L +           S+ A+++  + LE+ + E L++ S +   
Sbjct: 181  DEETESAVSSEDEDDELLTQAGDDDDEDGDESTEAEITVNDSLEEAR-EKLLELSQV--- 236

Query: 1044 FDKMRKAFEK-EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 1102
            F K++ A +K +   ++   K H+ +    +   F  K+++ +   L   +  +  IE++
Sbjct: 237  FKKLKTALDKGQSLATKKNQKLHDEVKQYFVAFSFPQKTMDLMEAQLEEPMEMIHAIERR 296

Query: 1103 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 1162
            ++ +V+ K GMPR  FI  FP +E +L WV  ++ ++  Y   L   I  ++  QQK + 
Sbjct: 297  LMRLVIEKSGMPRKSFISDFPGHETDLEWVVKQSTLRRKYAEKLKLMIEDVQAEQQKFLE 356

Query: 1163 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 1222
            ++    + +  ++DI R++  G+ +A++AK EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 357  VEKTYGMSIQQIKDIYRQLAVGKERAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQ 416

Query: 1223 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 1282
            EGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 417  EGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 476

Query: 1283 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342
            SR + Q+ G +P P  +++ M+MPE+KIRK+ KIAKEP+SME+P+GDDEDSHLGDF+ED 
Sbjct: 477  SRMLQQKNGRDPTPEELSVAMDMPEDKIRKVWKIAKEPISMETPIGDDEDSHLGDFLEDS 536

Query: 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402
            N+++P +AA    +     ++L SLTPRE +VLRMRFGI+M++DHTLEEVG+QFDVTRER
Sbjct: 537  NVISPLEAATTRGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRER 596

Query: 1403 IRQIEAKALRKLRHPSRYYKLKIFL 1427
            IRQIEAKALRKLRHP+R   LK FL
Sbjct: 597  IRQIEAKALRKLRHPNRSELLKSFL 621



 Score =  528 bits (1361), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 275/613 (44%), Positives = 406/613 (66%), Gaps = 34/613 (5%)

Query: 35  EIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL 94
           E +++ +++K L + G+E+G+LT+ EIN+ LPE  ++ E  + +I         ++E+ +
Sbjct: 9   EDDDVHEEYKELFEQGREQGFLTYEEINETLPESAVEGEKFDELIAF-------LNENGI 61

Query: 95  DTETLMLSNITS-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
           D          +  DD E      LS+ D++ GRT DP++MYMREMG+V+LLTR+GEI I
Sbjct: 62  DVVETPPEEEEAVTDDEESLANNVLSSADAEVGRTTDPVRMYMREMGAVDLLTREGEIAI 121

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE GL  +   ++  P  I  ++   +++   E ++ ++V+G  D  F+        
Sbjct: 122 AKRIESGLDLVQQTLAEFPLAIAALVAEFERVEAGEGRLSDLVNGYGDP-FAQKTEEATD 180

Query: 214 --------NKNNNEEKILIE-----------SSSADLST-EQLEKLKYESLIKFSNISFH 253
                   +  + ++++L +           S+ A+++  + LE+ + E L++ S +   
Sbjct: 181 DEETESAVSSEDEDDELLTQAGDDDDEDGDESTEAEITVNDSLEEAR-EKLLELSQV--- 236

Query: 254 FDKMRKAFEK-EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQ 312
           F K++ A +K +   ++   K H+ +    +   F  K+++ +   L   +  +  IE++
Sbjct: 237 FKKLKTALDKGQSLATKKNQKLHDEVKQYFVAFSFPQKTMDLMEAQLEEPMEMIHAIERR 296

Query: 313 ILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLIN 372
           ++ +V+ K GMPR  FI  FP +E +L WV  ++ ++  Y   L   I  ++  QQK + 
Sbjct: 297 LMRLVIEKSGMPRKSFISDFPGHETDLEWVVKQSTLRRKYAEKLKLMIEDVQAEQQKFLE 356

Query: 373 LQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQ 432
           ++    + +  ++DI R++  G+ +A++AK EM EANLRLVISIAKKYT+RGLQFLDLIQ
Sbjct: 357 VEKTYGMSIQQIKDIYRQLAVGKERAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQ 416

Query: 433 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRI 492
           EGNIGLMKAVDKFEYRRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RI
Sbjct: 417 EGNIGLMKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI 476

Query: 493 SRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552
           SR + Q+ G +P P  +++ M+MPE+KIRK+ KIAKEP+SME+P+GDDEDSHLGDF+ED 
Sbjct: 477 SRMLQQKNGRDPTPEELSVAMDMPEDKIRKVWKIAKEPISMETPIGDDEDSHLGDFLEDS 536

Query: 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612
           N+++P +AA    +     ++L SLTPRE +VLRMRFGI+M++DHTLEEVG+QFDVTRER
Sbjct: 537 NVISPLEAATTRGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRER 596

Query: 613 IRQIEAKALRKLR 625
           IRQIEAKALRKLR
Sbjct: 597 IRQIEAKALRKLR 609


>gi|258545971|ref|ZP_05706205.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
            ATCC 15826]
 gi|258518776|gb|EEV87635.1| DNA-directed RNA polymerase, sigmasubunit [Cardiobacterium hominis
            ATCC 15826]
          Length = 617

 Score =  540 bits (1392), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 285/610 (46%), Positives = 404/610 (66%), Gaps = 16/610 (2%)

Query: 828  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 887
            +++ + K L+  G+E+G+LT+ EI++ LPE  ++ +  + +I     M I V E   +  
Sbjct: 12   DVQDEVKELLARGREQGFLTYEEIHEALPEHALEGDKYDEMIALIVEMGIDVVESAQEDG 71

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
             +    I +DD+ E  + AAL+  +++ GRT DP++MYMREMG+V+LLTR+GEI IAKRI
Sbjct: 72   GV----IATDDEEEVPSAAALN--EAEIGRTTDPVRMYMREMGAVDLLTREGEIAIAKRI 125

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            E GL  +   ++  P  +  +L    KI   E ++ ++V+G  D   +     +  + ++
Sbjct: 126  EAGLNTVQQTLAEFPFAVSALLEEFAKIEAGEGRLSDLVNGYGDPYANKEEETLLESSDD 185

Query: 1008 NEEKILIESSSADLSTEQLEKLK---------YESLIKFSNISFHFDKMRKAFEK-EGYN 1057
             + + LI +   D   +    L+          E+  K   ++    K+  A  K +  +
Sbjct: 186  EDSETLISAGDDDEDDDSAAPLEEAPNNQDALLEAKEKLHELAAIHKKLMTALNKGKSLD 245

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
             +   K H  I   +    F  K+I+ +   L     ++  IE++++ +V+ + GMPR  
Sbjct: 246  DKKNQKLHGEIKEYIAAFSFPQKTIDLMEAQLNVAAEEIRDIERRLMRLVIERAGMPRKL 305

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI+ FP NE N +W+  ++K +  Y   L   I  I+  Q+K + ++    + +  L++I
Sbjct: 306  FIQEFPGNETNPDWIVGQSKQRRKYAEKLKGMITEIQVEQEKYLEIEKRYHMSILQLKEI 365

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
             +++  G+ +A++AK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 366  QKRLSMGKNQAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 425

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR ++Q+ G EP P 
Sbjct: 426  RRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRTLVQKNGREPTPE 485

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A  M+MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+++P +AA    + 
Sbjct: 486  ELAEAMDMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNVMSPLEAATTRGLS 545

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
                ++L SLTPRE +VLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLRHP
Sbjct: 546  EATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHP 605

Query: 1418 SRYYKLKIFL 1427
            +R   LK FL
Sbjct: 606  NRSELLKSFL 615



 Score =  527 bits (1357), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 278/598 (46%), Positives = 396/598 (66%), Gaps = 16/598 (2%)

Query: 38  NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE 97
           +++ + K L+  G+E+G+LT+ EI++ LPE  ++ +  + +I     M I V E   +  
Sbjct: 12  DVQDEVKELLARGREQGFLTYEEIHEALPEHALEGDKYDEMIALIVEMGIDVVESAQEDG 71

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
            +    I +DD+ E  + AAL+  +++ GRT DP++MYMREMG+V+LLTR+GEI IAKRI
Sbjct: 72  GV----IATDDEEEVPSAAALN--EAEIGRTTDPVRMYMREMGAVDLLTREGEIAIAKRI 125

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           E GL  +   ++  P  +  +L    KI   E ++ ++V+G  D   +     +  + ++
Sbjct: 126 EAGLNTVQQTLAEFPFAVSALLEEFAKIEAGEGRLSDLVNGYGDPYANKEEETLLESSDD 185

Query: 218 NEEKILIESSSADLSTEQLEKLK---------YESLIKFSNISFHFDKMRKAFEK-EGYN 267
            + + LI +   D   +    L+          E+  K   ++    K+  A  K +  +
Sbjct: 186 EDSETLISAGDDDEDDDSAAPLEEAPNNQDALLEAKEKLHELAAIHKKLMTALNKGKSLD 245

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
            +   K H  I   +    F  K+I+ +   L     ++  IE++++ +V+ + GMPR  
Sbjct: 246 DKKNQKLHGEIKEYIAAFSFPQKTIDLMEAQLNVAAEEIRDIERRLMRLVIERAGMPRKL 305

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI+ FP NE N +W+  ++K +  Y   L   I  I+  Q+K + ++    + +  L++I
Sbjct: 306 FIQEFPGNETNPDWIVGQSKQRRKYAEKLKGMITEIQVEQEKYLEIEKRYHMSILQLKEI 365

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
            +++  G+ +A++AK EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 366 QKRLSMGKNQAKRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 425

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRG+KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISR ++Q+ G EP P 
Sbjct: 426 RRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRTLVQKNGREPTPE 485

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A  M+MPEEKIRK++KIAKEP+SME+P+GDDEDSHLGDFIED N+++P +AA    + 
Sbjct: 486 ELAEAMDMPEEKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDSNVMSPLEAATTRGLS 545

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
               ++L SLTPRE +VLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLR
Sbjct: 546 EATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLR 603


>gi|406936817|gb|EKD70451.1| hypothetical protein ACD_46C00531G0001 [uncultured bacterium]
          Length = 533

 Score =  540 bits (1391), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 280/534 (52%), Positives = 367/534 (68%), Gaps = 28/534 (5%)

Query: 914  DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 973
            + GRT DP++MYMREMG VELL+R+GEI IAKRIEEG+  M+  ++  P  I E+L   D
Sbjct: 6    ELGRTTDPVRMYMREMGRVELLSREGEIAIAKRIEEGMNQMLTTLAYQPQMIAEVLADFD 65

Query: 974  KISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSA-------------- 1019
            ++ K E+++ +I+ G I+ N           +     K    +                 
Sbjct: 66   RVEKGELRLSDIISGYIEPNLEGEEGEGDDEEGAGTPKAAAPAPPVAVDEAEESEEAADP 125

Query: 1020 ---DLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 1075
               D   + ++ K ++E L KF N +   +K      K G   +  +   + ++   + I
Sbjct: 126  FDDDAGLDPVKAKERFEELRKFYNEAITTEK------KHGAKHKKTVVKRDELAKYFMDI 179

Query: 1076 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 1135
            + + +   KL   +R+ ++++   E+ I++  VNK  +PR  FI  F  NE NL W+   
Sbjct: 180  KLSPRQFNKLSRKMRSLLDEIRAQERAIMDYCVNKGKLPRKAFISAFVNNETNLEWL--- 236

Query: 1136 TKIQHDYNLI-LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 1194
            T+ Q    L  L + +P I   Q+KLI L+  + + + +++++NR++  GE KAR+AK+E
Sbjct: 237  TQSQSKAILAELEKFMPDIHRSQKKLIALEEQMRMNIAEIKEVNRRLSIGEAKARRAKKE 296

Query: 1195 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254
            M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+RGYKFSTYATWWIRQA
Sbjct: 297  MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQA 356

Query: 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 1314
            ITRSIADQARTIRIPVHMIETINK++RISRQ+LQETG EP P  ++ KM +PE+KIRKI+
Sbjct: 357  ITRSIADQARTIRIPVHMIETINKLNRISRQLLQETGLEPTPEELSRKMSIPEDKIRKIL 416

Query: 1315 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 1374
            KIAKEP+SME+P+GDDEDSHLGDFIED N ++P DAA N  +   V+ +L SLTPRE+KV
Sbjct: 417  KIAKEPISMETPIGDDEDSHLGDFIEDGNTISPIDAATNFGLSESVQKVLASLTPREAKV 476

Query: 1375 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            LRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ FLE
Sbjct: 477  LRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAEQLRSFLE 530



 Score =  523 bits (1347), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 272/521 (52%), Positives = 357/521 (68%), Gaps = 28/521 (5%)

Query: 124 DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 183
           + GRT DP++MYMREMG VELL+R+GEI IAKRIEEG+  M+  ++  P  I E+L   D
Sbjct: 6   ELGRTTDPVRMYMREMGRVELLSREGEIAIAKRIEEGMNQMLTTLAYQPQMIAEVLADFD 65

Query: 184 KISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSA-------------- 229
           ++ K E+++ +I+ G I+ N           +     K    +                 
Sbjct: 66  RVEKGELRLSDIISGYIEPNLEGEEGEGDDEEGAGTPKAAAPAPPVAVDEAEESEEAADP 125

Query: 230 ---DLSTEQLE-KLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGI 285
              D   + ++ K ++E L KF N +   +K      K G   +  +   + ++   + I
Sbjct: 126 FDDDAGLDPVKAKERFEELRKFYNEAITTEK------KHGAKHKKTVVKRDELAKYFMDI 179

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           + + +   KL   +R+ ++++   E+ I++  VNK  +PR  FI  F  NE NL W+   
Sbjct: 180 KLSPRQFNKLSRKMRSLLDEIRAQERAIMDYCVNKGKLPRKAFISAFVNNETNLEWL--- 236

Query: 346 TKIQHDYNLI-LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
           T+ Q    L  L + +P I   Q+KLI L+  + + + +++++NR++  GE KAR+AK+E
Sbjct: 237 TQSQSKAILAELEKFMPDIHRSQKKLIALEEQMRMNIAEIKEVNRRLSIGEAKARRAKKE 296

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY+RGYKFSTYATWWIRQA
Sbjct: 297 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQA 356

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++RISRQ+LQETG EP P  ++ KM +PE+KIRKI+
Sbjct: 357 ITRSIADQARTIRIPVHMIETINKLNRISRQLLQETGLEPTPEELSRKMSIPEDKIRKIL 416

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+SME+P+GDDEDSHLGDFIED N ++P DAA N  +   V+ +L SLTPRE+KV
Sbjct: 417 KIAKEPISMETPIGDDEDSHLGDFIEDGNTISPIDAATNFGLSESVQKVLASLTPREAKV 476

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 477 LRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 517


>gi|148827724|ref|YP_001292477.1| DNA primase [Haemophilus influenzae PittGG]
 gi|148718966|gb|ABR00094.1| DNA primase [Haemophilus influenzae PittGG]
          Length = 629

 Score =  540 bits (1390), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 306/639 (47%), Positives = 413/639 (64%), Gaps = 39/639 (6%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 996  SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 1035
              N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175  DPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 1036 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 1089
             KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235  EKFQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290  KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITANGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
               I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350  EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470  VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530  DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 590  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  525 bits (1352), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 299/626 (47%), Positives = 404/626 (64%), Gaps = 39/626 (6%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 206 SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 245
             N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175 DPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 246 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 299
            KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235 EKFQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
           +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290 KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITANGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
              I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350 EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470 VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530 DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 590 EEVGKQFDVTRERIRQIEAKALRKLR 615


>gi|16272477|ref|NP_438691.1| RNA polymerase sigma-70 factor [Haemophilus influenzae Rd KW20]
 gi|260580980|ref|ZP_05848803.1| transcription initiation factor sigma 70 [Haemophilus influenzae
            RdAW]
 gi|1173125|sp|P43766.1|RPOD_HAEIN RecName: Full=RNA polymerase sigma factor RpoD; AltName:
            Full=Sigma-70
 gi|1573517|gb|AAC22190.1| RNA polymerase sigma-70 factor (rpoD) [Haemophilus influenzae Rd
            KW20]
 gi|260092339|gb|EEW76279.1| transcription initiation factor sigma 70 [Haemophilus influenzae
            RdAW]
          Length = 629

 Score =  540 bits (1390), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 301/634 (47%), Positives = 410/634 (64%), Gaps = 29/634 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--------- 986
            TR+ EI IAKRIE G+ ++  +IS+ P  +  +L   D + K   ++ +++         
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 987  ----DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSN 1039
                +GL +     ++     N +  + +   ++ S   S         +  +   KF  
Sbjct: 180  IEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQ 239

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQIN 1094
            +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  + 
Sbjct: 240  LREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMK 294

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
            +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I 
Sbjct: 295  RVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIY 354

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
            E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 355  EALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRG 414

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 415  LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 474

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSH
Sbjct: 475  TINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSH 534

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGK
Sbjct: 535  LGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGK 594

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            QFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  QFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  525 bits (1351), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 294/621 (47%), Positives = 401/621 (64%), Gaps = 29/621 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--------- 196
           TR+ EI IAKRIE G+ ++  +IS+ P  +  +L   D + K   ++ +++         
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSISAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 197 ----DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSN 249
               +GL +     ++     N +  + +   ++ S   S         +  +   KF  
Sbjct: 180 IEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQ 239

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQIN 304
           +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  + 
Sbjct: 240 LREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMK 294

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
           +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I 
Sbjct: 295 RVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIY 354

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 355 EALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRG 414

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 415 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 474

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSH
Sbjct: 475 TINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSH 534

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGK
Sbjct: 535 LGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGK 594

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKALRKLR
Sbjct: 595 QFDVTRERIRQIEAKALRKLR 615


>gi|145638551|ref|ZP_01794160.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229844308|ref|ZP_04464448.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|229846616|ref|ZP_04466724.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|386265080|ref|YP_005828572.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2846]
 gi|145272146|gb|EDK12054.1| aspartate ammonia-lyase [Haemophilus influenzae PittII]
 gi|229810709|gb|EEP46427.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 7P49H1]
 gi|229812557|gb|EEP48246.1| RNA polymerase sigma-70 factor [Haemophilus influenzae 6P18H1]
 gi|309750056|gb|ADO80040.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2866]
 gi|309972316|gb|ADO95517.1| RNA polymerase sigma-70 factor [Haemophilus influenzae R2846]
          Length = 629

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 306/639 (47%), Positives = 413/639 (64%), Gaps = 39/639 (6%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 996  SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 1035
              N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175  DPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 1036 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 1089
             KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235  EKFQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290  KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
               I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350  EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470  VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530  DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 590  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  525 bits (1351), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 299/626 (47%), Positives = 404/626 (64%), Gaps = 39/626 (6%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 206 SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 245
             N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175 DPNAEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 246 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 299
            KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235 EKFQQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
           +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290 KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
              I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350 EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470 VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530 DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 590 EEVGKQFDVTRERIRQIEAKALRKLR 615


>gi|319775546|ref|YP_004138034.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
            F3047]
 gi|317450137|emb|CBY86351.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
            F3047]
          Length = 629

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 306/636 (48%), Positives = 411/636 (64%), Gaps = 39/636 (6%)

Query: 821  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 879
            N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 4    NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 63

Query: 880  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
             +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 64   LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 122

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 998
             EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N
Sbjct: 123  DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPN 177

Query: 999  RVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
              I+ +       ++E    ESS+AD+   + E+                        KF
Sbjct: 178  AEIEEHNGLDEDFSDEDDEEESSNADVENNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 238  QQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 292

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 293  MKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDR 352

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 353  IYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 412

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 413  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 472

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 473  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 532

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 533  SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 592

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 593  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  524 bits (1350), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 299/623 (47%), Positives = 402/623 (64%), Gaps = 39/623 (6%)

Query: 31  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 89
           N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 4   NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 63

Query: 90  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
            +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 64  LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 122

Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 208
            EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N
Sbjct: 123 DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPN 177

Query: 209 RVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
             I+ +       ++E    ESS+AD+   + E+                        KF
Sbjct: 178 AEIEEHNGLDEDFSDEDDEEESSNADVENNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 238 QQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 292

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 293 MKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDR 352

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 353 IYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 412

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 413 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 472

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 473 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 532

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 533 SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 592

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 593 GKQFDVTRERIRQIEAKALRKLR 615


>gi|319897950|ref|YP_004136147.1| RNA polymerase, sigma 70 (sigma d) factor [Haemophilus influenzae
            F3031]
 gi|329122411|ref|ZP_08250998.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus aegyptius
            ATCC 11116]
 gi|317433456|emb|CBY81839.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
            F3031]
 gi|327473693|gb|EGF19112.1| DNA-directed RNA polymerase sigma subunit RpoD [Haemophilus aegyptius
            ATCC 11116]
          Length = 629

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 306/636 (48%), Positives = 411/636 (64%), Gaps = 39/636 (6%)

Query: 821  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 879
            N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 4    NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 63

Query: 880  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
             +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 64   LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 122

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 998
             EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N
Sbjct: 123  DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPN 177

Query: 999  RVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 1037
              I+ +       ++E    ESS+AD+   + E+                        KF
Sbjct: 178  AEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 1092
              +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 238  QQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 292

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 1152
            + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 293  MKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDR 352

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 353  IYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 412

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 413  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 472

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 473  IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 532

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 533  SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 592

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 593  GKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  524 bits (1350), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 299/623 (47%), Positives = 402/623 (64%), Gaps = 39/623 (6%)

Query: 31  NSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISV 89
           N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V
Sbjct: 4   NQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPV 63

Query: 90  SEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
            +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+
Sbjct: 64  LDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTRE 122

Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN 208
            EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N
Sbjct: 123 DEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPN 177

Query: 209 RVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KF 247
             I+ +       ++E    ESS+AD+   + E+                        KF
Sbjct: 178 AEIEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKF 237

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQ 302
             +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  
Sbjct: 238 QQLREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEM 292

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPS 362
           + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    
Sbjct: 293 MKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDR 352

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+
Sbjct: 353 IYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN 412

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 413 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 472

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+D
Sbjct: 473 IETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDD 532

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEV
Sbjct: 533 SHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEV 592

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           GKQFDVTRERIRQIEAKALRKLR
Sbjct: 593 GKQFDVTRERIRQIEAKALRKLR 615


>gi|378696729|ref|YP_005178687.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
            10810]
 gi|301169248|emb|CBW28845.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
            10810]
          Length = 629

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 306/639 (47%), Positives = 413/639 (64%), Gaps = 39/639 (6%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 995
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 996  SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 1035
              N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175  DPNAEIEEHSGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 1036 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 1089
             KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235  EKFQQLREQHSKTLAVIEKHGRSEK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
            +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290  KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
               I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350  EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470  VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530  DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 590  EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  524 bits (1350), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 299/626 (47%), Positives = 404/626 (64%), Gaps = 39/626 (6%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS 205
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F 
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FV 174

Query: 206 SNNRVIKGNKN----NNEEKILIESSSADLSTEQLEKLKYESLI---------------- 245
             N  I+ +       ++E    ESS+AD+   + E+                       
Sbjct: 175 DPNAEIEEHSGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAR 234

Query: 246 -KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTL 299
            KF  +     K     EK G + +   +A + I+  +LG      R   K  + L  ++
Sbjct: 235 EKFQQLREQHSKTLAVIEKHGRSEK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSM 289

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
           +  + +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L + 
Sbjct: 290 KEMMKRVRYQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKY 349

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
              I E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKK
Sbjct: 350 EDRIYEALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKK 409

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 410 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 469

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GD
Sbjct: 470 VHMIETINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGD 529

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           D+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTL
Sbjct: 530 DDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 590 EEVGKQFDVTRERIRQIEAKALRKLR 615


>gi|145640511|ref|ZP_01796095.1| DNA primase [Haemophilus influenzae R3021]
 gi|145275097|gb|EDK14959.1| DNA primase [Haemophilus influenzae 22.4-21]
          Length = 629

 Score =  539 bits (1389), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 300/634 (47%), Positives = 410/634 (64%), Gaps = 29/634 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 876
            ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1    MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 877  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 935
            I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61   IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--------- 986
            TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++         
Sbjct: 120  TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 987  ----DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSN 1039
                +GL +     ++     N +  + +   ++ S   S         +  +   KF  
Sbjct: 180  IEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQ 239

Query: 1040 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQIN 1094
            +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  + 
Sbjct: 240  LREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMK 294

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
            +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I 
Sbjct: 295  RVRNQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIY 354

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
            E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 355  EALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRG 414

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 415  LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 474

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSH
Sbjct: 475  TINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSH 534

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGK
Sbjct: 535  LGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGK 594

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            QFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 595  QFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  524 bits (1350), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 293/621 (47%), Positives = 401/621 (64%), Gaps = 29/621 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MD 86
           ++ N +   E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    
Sbjct: 1   MEKNQQSTAEQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAG 60

Query: 87  ISVSEHVLDTETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELL 145
           I V +   +++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LL
Sbjct: 61  IPVLDEAPESDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLL 119

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--------- 196
           TR+ EI IAKRIE G+ ++  +I++ P  +  +L   D + K   ++ +++         
Sbjct: 120 TREDEISIAKRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITGFVDPNAE 179

Query: 197 ----DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---KFSN 249
               +GL +     ++     N +  + +   ++ S   S         +  +   KF  
Sbjct: 180 IEEHNGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQ 239

Query: 250 ISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQIN 304
           +     K     EK G + +   +A + I+  +LG      R   K  + L  +++  + 
Sbjct: 240 LREQHSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMK 294

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
           +V   E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I 
Sbjct: 295 RVRNQERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIY 354

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           E    L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RG
Sbjct: 355 EALNNLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRG 414

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 415 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 474

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSH
Sbjct: 475 TINKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSH 534

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGK
Sbjct: 535 LGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGK 594

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QFDVTRERIRQIEAKALRKLR
Sbjct: 595 QFDVTRERIRQIEAKALRKLR 615


>gi|145637426|ref|ZP_01793085.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
 gi|145269372|gb|EDK09316.1| aspartate ammonia-lyase [Haemophilus influenzae PittHH]
          Length = 629

 Score =  538 bits (1386), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 305/630 (48%), Positives = 409/630 (64%), Gaps = 39/630 (6%)

Query: 827  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISVSEHVLD 885
            E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V +   +
Sbjct: 10   EQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPE 69

Query: 886  TETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 944
            ++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+ EI IA
Sbjct: 70   SDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTREDEISIA 128

Query: 945  KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 1004
            KRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N  I+ +
Sbjct: 129  KRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPNAEIEEH 183

Query: 1005 KN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFH 1043
                   ++E    ESS+AD+   + E+                        KF  +   
Sbjct: 184  NGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQLREQ 243

Query: 1044 FDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQ 1098
              K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V  
Sbjct: 244  HSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRY 298

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
             E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E   
Sbjct: 299  QERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALN 358

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
             L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 359  NLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 418

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 419  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 478

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            ++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 479  LNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 538

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 539  IEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 598

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 599  TRERIRQIEAKALRKLRHPSRSETLRSFLD 628



 Score =  523 bits (1348), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 298/617 (48%), Positives = 400/617 (64%), Gaps = 39/617 (6%)

Query: 37  ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRY-MDISVSEHVLD 95
           E   ++ + L++LG+ +GYLTF+EIND LPED ID E  + +++T +    I V +   +
Sbjct: 10  EQYSEQIEQLMELGRTQGYLTFAEINDLLPEDAIDPEYYDKLLQTLQNDAGIPVLDEAPE 69

Query: 96  TETLMLSNITSDDD-VEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIA 154
           ++ +MLS+   D+D VEEAT+  LS V+S+ GRT DP++MYMREMG+V+LLTR+ EI IA
Sbjct: 70  SDDMMLSDTIPDEDAVEEATQI-LSNVESEIGRTTDPVRMYMREMGTVDLLTREDEISIA 128

Query: 155 KRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN 214
           KRIE G+ ++  +I++ P  +  +L   D + K   ++ +++ G     F   N  I+ +
Sbjct: 129 KRIEGGIDEVQTSIAAYPEALNGLLKNYDDVEKGNFRLTDLITG-----FVDPNAEIEEH 183

Query: 215 KN----NNEEKILIESSSADLSTEQLEKLKYESLI-----------------KFSNISFH 253
                  ++E    ESS+AD+   + E+                        KF  +   
Sbjct: 184 NGLDEDFSDEDDEEESSNADVEDNEDEEDNESESTSDSSDSDNSIDPEVAREKFQQLREQ 243

Query: 254 FDKMRKAFEKEGYNSESYIKAHNNISNEMLG-----IRFTAKSIEKLCDTLRNQINQVTQ 308
             K     EK G + +   +A + I+  +LG      R   K  + L  +++  + +V  
Sbjct: 244 HSKTLAVIEKHGRSGK---RAQDQIA--LLGEIFKQFRLVPKQFDLLVLSMKEMMKRVRY 298

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
            E+Q+ +I+V+  GMP+  F K+   N  N  WV    K    +   L +    I E   
Sbjct: 299 QERQLQKILVDIAGMPKDDFEKIITTNGSNSEWVAKALKSSKPWAKRLIKYEDRIYEALN 358

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
            L   + +  L +  +RDI   +  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 359 NLAITEENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 418

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 419 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 478

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           ++RISRQ+LQE G E  P  +A +M MPE+KIRK++KIAKEP+SME+P+GDD+DSHLGDF
Sbjct: 479 LNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDF 538

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED  +  P D+A   S++    ++L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDV
Sbjct: 539 IEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 598

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKLR
Sbjct: 599 TRERIRQIEAKALRKLR 615


>gi|91227144|ref|ZP_01261628.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|91188796|gb|EAS75083.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
          Length = 574

 Score =  537 bits (1384), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 282/538 (52%), Positives = 370/538 (68%), Gaps = 21/538 (3%)

Query: 908  LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 967
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+  +  +++  P TI  
Sbjct: 40   LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPY 99

Query: 968  ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 1027
            IL   DK+   E+++ +++ G +D + + +          +E   L ES   +   E ++
Sbjct: 100  ILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTATHIGSE---LTESQLEEEDDEDVD 155

Query: 1028 KLKYE-----------------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 1070
              +                   +L KF+ +   +  ++ A  + GYNS     A+  + +
Sbjct: 156  DDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNLQLAINEYGYNSPKATVANEMMLD 215

Query: 1071 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 1130
                 R T K  + L + LR  +++V   E+ I++ VV    MP+  FI +F  NE +  
Sbjct: 216  VFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEA 275

Query: 1131 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 1190
            W+D        Y   + RN   I+    KL  ++ +  L + +++DI+R+M  GE KAR+
Sbjct: 276  WLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARR 335

Query: 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250
            AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 336  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 395

Query: 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310
            IRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KI
Sbjct: 396  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKI 455

Query: 1311 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 1370
            RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S++   KD+L  LTPR
Sbjct: 456  RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPR 515

Query: 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            E+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 516  EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 573



 Score =  523 bits (1346), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 275/525 (52%), Positives = 361/525 (68%), Gaps = 21/525 (4%)

Query: 118 LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 177
           LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIEEG+  +  +++  P TI  
Sbjct: 40  LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEEGINQVQSSVAEYPGTIPY 99

Query: 178 ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 237
           IL   DK+   E+++ +++ G +D + + +          +E   L ES   +   E ++
Sbjct: 100 ILEQFDKVQAEELRLTDLISGFVDPD-ADDTAAPTATHIGSE---LTESQLEEEDDEDVD 155

Query: 238 KLKYE-----------------SLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISN 280
             +                   +L KF+ +   +  ++ A  + GYNS     A+  + +
Sbjct: 156 DDEDSDDDSDDSEEDVGIDPELALEKFNQLRSTYQNLQLAINEYGYNSPKATVANEMMLD 215

Query: 281 EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLN 340
                R T K  + L + LR  +++V   E+ I++ VV    MP+  FI +F  NE +  
Sbjct: 216 VFREFRLTPKQFDHLVNELRTAMDRVRTQERLIMKSVVEYGKMPKKSFIALFTGNESSEA 275

Query: 341 WVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARK 400
           W+D        Y   + RN   I+    KL  ++ +  L + +++DI+R+M  GE KAR+
Sbjct: 276 WLDEVLASDKPYAEKIKRNEEEIRRSIAKLKMIEEETSLNVQNIKDISRRMSIGEAKARR 335

Query: 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460
           AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
Sbjct: 336 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 395

Query: 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 520
           IRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KI
Sbjct: 396 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKI 455

Query: 521 RKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPR 580
           RK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S++   KD+L  LTPR
Sbjct: 456 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKVATKDVLAGLTPR 515

Query: 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           E+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 516 EAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 560


>gi|116514979|ref|YP_802608.1| RNA polymerase major s factor [Buchnera aphidicola BCc]
 gi|116256833|gb|ABJ90515.1| RNA polymerase major s factor [Buchnera aphidicola BCc]
          Length = 613

 Score =  536 bits (1381), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 305/612 (49%), Positives = 420/612 (68%), Gaps = 19/612 (3%)

Query: 830  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 889
            + + K+L+  GKE+GYLT+SE++D LP DI+D + I++II+  + + I + E V + E L
Sbjct: 6    KSQLKLLVSHGKEQGYLTYSEVHDHLPNDIVDADQIKNIIQMIKDLGIQIVEEVREIEEL 65

Query: 890  MLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +++   +D  +D  EA    LS V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 66   IINEAPTDTDEDTVEAATQVLSNVETEIGRTTDPVRMYMREMGTVELLTREGEIGIAKRI 125

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----NNRVIK 1002
            EEG+  +  ++S  PT+I+ +L     +    IK+ E++ G IDK            VI 
Sbjct: 126  EEGINQVQSSVSEYPTSILYLLEQYHHVKLGNIKLSELIIGFIDKKKKPKKKIFTEEVIT 185

Query: 1003 GNKNNNEEKILIESSSADLSTEQ------LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 1056
                NN++K L    + D   +       L K K+  L K   I+ H        + +  
Sbjct: 186  KKLYNNKKKSLNAEKNEDTIDDYNHIDPILAKKKFSQLKKQYYITNHI------IQNKPR 239

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
            N +  I A + +S      R   K  + L   +RN+I+++T  EK+I+ + V+ C +P+ 
Sbjct: 240  NHKDSINAIHKLSKIFKQFRLAPKQFDYLVTNMRNEIHKITLQEKKIMNLCVHTCKIPKK 299

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 1176
             F+K F +++ N     +  K +  +   L      I +  +KL+ ++    L +  ++D
Sbjct: 300  KFLKFFKKHKKNYKNFYSVIKKKKSWLYKLKFIKKEIIKRIKKLLIIEKKTKLKITQIKD 359

Query: 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236
            IN+++I GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 360  INKRIILGEEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 419

Query: 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 1296
            YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 420  YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTP 479

Query: 1297 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356
              ++ KM + EEKIRK++KIAKEP+SME+P+G+D+D+HLGDFIED N+  P ++A + S+
Sbjct: 480  EELSEKMLISEEKIRKVLKIAKEPISMETPIGEDDDTHLGDFIEDTNLELPLESATSESL 539

Query: 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416
            +++  D+L+ LT RE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLRH
Sbjct: 540  KTITNDVLSGLTDREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRH 599

Query: 1417 PSRYYKLKIFLE 1428
            PSR   LK FL+
Sbjct: 600  PSRSEILKSFLD 611



 Score =  522 bits (1345), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 297/599 (49%), Positives = 411/599 (68%), Gaps = 19/599 (3%)

Query: 40  RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL 99
           + + K+L+  GKE+GYLT+SE++D LP DI+D + I++II+  + + I + E V + E L
Sbjct: 6   KSQLKLLVSHGKEQGYLTYSEVHDHLPNDIVDADQIKNIIQMIKDLGIQIVEEVREIEEL 65

Query: 100 MLSNITSD--DDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +++   +D  +D  EA    LS V+++ GRT DP++MYMREMG+VELLTR+GEI IAKRI
Sbjct: 66  IINEAPTDTDEDTVEAATQVLSNVETEIGRTTDPVRMYMREMGTVELLTREGEIGIAKRI 125

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-----NNRVIK 212
           EEG+  +  ++S  PT+I+ +L     +    IK+ E++ G IDK            VI 
Sbjct: 126 EEGINQVQSSVSEYPTSILYLLEQYHHVKLGNIKLSELIIGFIDKKKKPKKKIFTEEVIT 185

Query: 213 GNKNNNEEKILIESSSADLSTEQ------LEKLKYESLIKFSNISFHFDKMRKAFEKEGY 266
               NN++K L    + D   +       L K K+  L K   I+ H        + +  
Sbjct: 186 KKLYNNKKKSLNAEKNEDTIDDYNHIDPILAKKKFSQLKKQYYITNHI------IQNKPR 239

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
           N +  I A + +S      R   K  + L   +RN+I+++T  EK+I+ + V+ C +P+ 
Sbjct: 240 NHKDSINAIHKLSKIFKQFRLAPKQFDYLVTNMRNEIHKITLQEKKIMNLCVHTCKIPKK 299

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRD 386
            F+K F +++ N     +  K +  +   L      I +  +KL+ ++    L +  ++D
Sbjct: 300 KFLKFFKKHKKNYKNFYSVIKKKKSWLYKLKFIKKEIIKRIKKLLIIEKKTKLKITQIKD 359

Query: 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 446
           IN+++I GE KA++AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFE
Sbjct: 360 INKRIILGEEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 419

Query: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDP 506
           YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P
Sbjct: 420 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTP 479

Query: 507 SVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566
             ++ KM + EEKIRK++KIAKEP+SME+P+G+D+D+HLGDFIED N+  P ++A + S+
Sbjct: 480 EELSEKMLISEEKIRKVLKIAKEPISMETPIGEDDDTHLGDFIEDTNLELPLESATSESL 539

Query: 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +++  D+L+ LT RE+KVLRMRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLR
Sbjct: 540 KTITNDVLSGLTDREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLR 598


>gi|153828433|ref|ZP_01981100.1| RNA polymerase sigma factor RpoD, partial [Vibrio cholerae 623-39]
 gi|148876142|gb|EDL74277.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
          Length = 572

 Score =  535 bits (1379), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 283/548 (51%), Positives = 368/548 (67%), Gaps = 34/548 (6%)

Query: 908  LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 967
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  
Sbjct: 31   LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPY 90

Query: 968  ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 1027
            IL   D++   E+++ +++ G +D N           +      I  E S ADL+ E   
Sbjct: 91   ILEQFDRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDA 143

Query: 1028 KLKYESLI---------------------------KFSNISFHFDKMRKAFEKEGYNSES 1060
             ++ E                              KF+ +   F  ++ A  + G +S  
Sbjct: 144  VVEDEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQ 203

Query: 1061 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 1120
              +A + + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI 
Sbjct: 204  ASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIA 263

Query: 1121 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 1180
            +F  NE N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+
Sbjct: 264  LFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRR 323

Query: 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 1240
            M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 324  MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 383

Query: 1241 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 1300
            YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 384  YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 443

Query: 1301 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 1360
             +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  
Sbjct: 444  ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 503

Query: 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420
            +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 
Sbjct: 504  RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 563

Query: 1421 YKLKIFLE 1428
              L+ FL+
Sbjct: 564  EVLRSFLD 571



 Score =  521 bits (1342), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 276/535 (51%), Positives = 359/535 (67%), Gaps = 34/535 (6%)

Query: 118 LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 177
           LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  
Sbjct: 31  LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPY 90

Query: 178 ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 237
           IL   D++   E+++ +++ G +D N           +      I  E S ADL+ E   
Sbjct: 91  ILEQFDRVQAEELRLTDLISGFVDPNDMET-------EAPTATHIGSELSEADLADEDDA 143

Query: 238 KLKYESLI---------------------------KFSNISFHFDKMRKAFEKEGYNSES 270
            ++ E                              KF+ +   F  ++ A  + G +S  
Sbjct: 144 VVEDEDEDEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQ 203

Query: 271 YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIK 330
             +A + + +     R T K  + L +TLR  +++V   E+ +++ VV    MP+  FI 
Sbjct: 204 ASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIA 263

Query: 331 VFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRK 390
           +F  NE N  W+D        Y   +      I+   QKL  ++ +  L +  ++DI+R+
Sbjct: 264 LFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRR 323

Query: 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRG 450
           M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRG
Sbjct: 324 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 383

Query: 451 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIA 510
           YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A
Sbjct: 384 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 443

Query: 511 IKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVV 570
            +M+MPE+KIRK++KIAKEP+SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  
Sbjct: 444 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 503

Query: 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +D+L  LTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 504 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 558


>gi|403049305|ref|ZP_10903789.1| transcription initiation factor sigma 70 [SAR86 cluster bacterium
            SAR86D]
          Length = 604

 Score =  535 bits (1378), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 282/594 (47%), Positives = 397/594 (66%), Gaps = 5/594 (0%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D + L+L+   
Sbjct: 14   LIVKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADDLLLAESE 73

Query: 896  SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
              DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D+
Sbjct: 74   DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRDL 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            + A  + P T+  ++     +   E KI++ + G +++     +      +   E +   
Sbjct: 134  LAASVAYPRTVEYVIDYHQMVKDGEKKINDFLTGFLEEMEEVPSAGPGSQRAKEEAEAAE 193

Query: 1015 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 1074
            ES     S   +++++     + +N+   ++K  K  E +G +S+        +      
Sbjct: 194  ESDDDAPSGPDMQEVQR----RMTNLKRQYNKTLKTIESKGRHSKEANADFQKLGEIFQF 249

Query: 1075 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 1134
            ++F+ +  + +    R+ ++ + + EK I E +V    MPR  F+  + +N   + WVD+
Sbjct: 250  LKFSPRMFDDIASIARSGLSNIREKEKFIQEQLVRNARMPRKDFLASYTDNLTKVRWVDS 309

Query: 1135 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 1194
              K +     +L +    +   Q+ +I L+  + L + ++++INR M  GE K R+AK++
Sbjct: 310  LMKEKKYKKDLLEKVKQDVVIAQKNIIELEQRVGLSVKEIKEINRSMSMGETKMRRAKKD 369

Query: 1195 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254
            M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 370  MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 429

Query: 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 1314
            ITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK++
Sbjct: 430  ITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKVL 489

Query: 1315 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 1374
            KIAKEP+S E+P+GDDEDS LGDFIED  + +P   A   S+     D+L SLT RE+KV
Sbjct: 490  KIAKEPISTETPIGDDEDSSLGDFIEDTVIESPLQNATEDSLHFATDDVLASLTAREAKV 549

Query: 1375 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            LRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   LK FL+
Sbjct: 550  LRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSSHLKSFLD 603



 Score =  519 bits (1337), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 274/581 (47%), Positives = 388/581 (66%), Gaps = 5/581 (0%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D + L+L+   
Sbjct: 14  LIVKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADDLLLAESE 73

Query: 106 SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
             DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++D+
Sbjct: 74  DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMRDL 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           + A  + P T+  ++     +   E KI++ + G +++     +      +   E +   
Sbjct: 134 LAASVAYPRTVEYVIDYHQMVKDGEKKINDFLTGFLEEMEEVPSAGPGSQRAKEEAEAAE 193

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
           ES     S   +++++     + +N+   ++K  K  E +G +S+        +      
Sbjct: 194 ESDDDAPSGPDMQEVQR----RMTNLKRQYNKTLKTIESKGRHSKEANADFQKLGEIFQF 249

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           ++F+ +  + +    R+ ++ + + EK I E +V    MPR  F+  + +N   + WVD+
Sbjct: 250 LKFSPRMFDDIASIARSGLSNIREKEKFIQEQLVRNARMPRKDFLASYTDNLTKVRWVDS 309

Query: 345 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKRE 404
             K +     +L +    +   Q+ +I L+  + L + ++++INR M  GE K R+AK++
Sbjct: 310 LMKEKKYKKDLLEKVKQDVVIAQKNIIELEQRVGLSVKEIKEINRSMSMGETKMRRAKKD 369

Query: 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464
           M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA
Sbjct: 370 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 429

Query: 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524
           ITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK++
Sbjct: 430 ITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKVL 489

Query: 525 KIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 584
           KIAKEP+S E+P+GDDEDS LGDFIED  + +P   A   S+     D+L SLT RE+KV
Sbjct: 490 KIAKEPISTETPIGDDEDSSLGDFIEDTVIESPLQNATEDSLHFATDDVLASLTAREAKV 549

Query: 585 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           LRMRFGI M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 550 LRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 590


>gi|356960539|ref|ZP_09063521.1| RNA polymerase, sigma 70 subunit, RpoD [gamma proteobacterium SCGC
            AAA001-B15]
          Length = 612

 Score =  535 bits (1377), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 296/616 (48%), Positives = 406/616 (65%), Gaps = 41/616 (6%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 894
            LI +GKE+GYLT+SEIND LPED++  E +E I+     +DI V++   D++TL++ S  
Sbjct: 15   LITIGKEQGYLTYSEINDLLPEDLLTPEQVEPIVTILEELDIVVADEAPDSDTLVMESGG 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             +     E   AAL+ +DS+FGRT DP++MYMREMG VELL +  E+ IAK IE G+  +
Sbjct: 75   KAQASSAEVAVAALAALDSEFGRTTDPVRMYMREMGVVELLEQKDEVRIAKEIEAGVYLI 134

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK-IL 1013
            + AIS  P        A  ++ + + KI ++V G             +G+    EEK  +
Sbjct: 135  MQAISLYPEISDYFFRAYTRLEEGKCKITDVVIGY------------QGDAEEFEEKQAI 182

Query: 1014 IESSSADLSTEQLEKLKYESLIKFSNISF----------HFDKMRKAFEK-------EGY 1056
            I    A L   +L++   E   +F  + +           F+K++K F+         GY
Sbjct: 183  IMEKQAQLEEMELDETIEEEGEEFDELEYTGPNEGEVYERFEKIKKTFKSYSRSNINNGY 242

Query: 1057 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 1116
                 IKA    S  +  +R   K +  + + + +++++V + E  I +  ++  GMPR 
Sbjct: 243  LDNKTIKARQKFSESISELRLAPKLVSTMMEVVSHRVDEVKKEENVIRQACLD-AGMPRQ 301

Query: 1117 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVLPLN 1172
             F   FP NE N +W+        ++++ L + + + K+     Q+ L+  +  + + + 
Sbjct: 302  LFYDSFPGNETNFDWL-----TLPNFDITLKKALKAHKDHIYYAQKSLLEHEISMQISIP 356

Query: 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232
            +L+DIN+K+  G+ KA+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAV
Sbjct: 357  ELKDINKKLRQGDRKAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAV 416

Query: 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 1292
            DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ  G 
Sbjct: 417  DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQRYGR 476

Query: 1293 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352
            E  P  +AI+ME+PE KI KI+KIAKEP+SME+PVGDDEDS +GDFIEDE + +P +   
Sbjct: 477  EATPEELAIEMELPEYKINKILKIAKEPLSMENPVGDDEDSTIGDFIEDEKLSSPVEVTT 536

Query: 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412
              S++    D+L +L+PRE+KVL+MRFGI+MS+DHTLEEVG+QFDVTRERIRQIEAKALR
Sbjct: 537  RESLKETTGDLLANLSPREAKVLKMRFGIDMSTDHTLEEVGRQFDVTRERIRQIEAKALR 596

Query: 1413 KLRHPSRYYKLKIFLE 1428
            KLRHPSR +KL+ FLE
Sbjct: 597  KLRHPSRAHKLQSFLE 612



 Score =  515 bits (1327), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 287/603 (47%), Positives = 395/603 (65%), Gaps = 41/603 (6%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 104
           LI +GKE+GYLT+SEIND LPED++  E +E I+     +DI V++   D++TL++ S  
Sbjct: 15  LITIGKEQGYLTYSEINDLLPEDLLTPEQVEPIVTILEELDIVVADEAPDSDTLVMESGG 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            +     E   AAL+ +DS+FGRT DP++MYMREMG VELL +  E+ IAK IE G+  +
Sbjct: 75  KAQASSAEVAVAALAALDSEFGRTTDPVRMYMREMGVVELLEQKDEVRIAKEIEAGVYLI 134

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK-IL 223
           + AIS  P        A  ++ + + KI ++V G             +G+    EEK  +
Sbjct: 135 MQAISLYPEISDYFFRAYTRLEEGKCKITDVVIGY------------QGDAEEFEEKQAI 182

Query: 224 IESSSADLSTEQLEKLKYESLIKFSNISF----------HFDKMRKAFEK-------EGY 266
           I    A L   +L++   E   +F  + +           F+K++K F+         GY
Sbjct: 183 IMEKQAQLEEMELDETIEEEGEEFDELEYTGPNEGEVYERFEKIKKTFKSYSRSNINNGY 242

Query: 267 NSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRL 326
                IKA    S  +  +R   K +  + + + +++++V + E  I +  ++  GMPR 
Sbjct: 243 LDNKTIKARQKFSESISELRLAPKLVSTMMEVVSHRVDEVKKEENVIRQACLD-AGMPRQ 301

Query: 327 HFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKE----LQQKLINLQTDIVLPLN 382
            F   FP NE N +W+        ++++ L + + + K+     Q+ L+  +  + + + 
Sbjct: 302 LFYDSFPGNETNFDWL-----TLPNFDITLKKALKAHKDHIYYAQKSLLEHEISMQISIP 356

Query: 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 442
           +L+DIN+K+  G+ KA+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAV
Sbjct: 357 ELKDINKKLRQGDRKAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAV 416

Query: 443 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502
           DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ  G 
Sbjct: 417 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQRYGR 476

Query: 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562
           E  P  +AI+ME+PE KI KI+KIAKEP+SME+PVGDDEDS +GDFIEDE + +P +   
Sbjct: 477 EATPEELAIEMELPEYKINKILKIAKEPLSMENPVGDDEDSTIGDFIEDEKLSSPVEVTT 536

Query: 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622
             S++    D+L +L+PRE+KVL+MRFGI+MS+DHTLEEVG+QFDVTRERIRQIEAKALR
Sbjct: 537 RESLKETTGDLLANLSPREAKVLKMRFGIDMSTDHTLEEVGRQFDVTRERIRQIEAKALR 596

Query: 623 KLR 625
           KLR
Sbjct: 597 KLR 599


>gi|420256712|ref|ZP_14759540.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
 gi|398042665|gb|EJL35650.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia sp. BT03]
          Length = 519

 Score =  535 bits (1377), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 261/509 (51%), Positives = 356/509 (69%), Gaps = 9/509 (1%)

Query: 927  REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986
            REMG+ ELLTR GE+ +A+RIE+G  D + AI+SCPTTI ++L  AD ++     I+E V
Sbjct: 7    REMGATELLTRQGEVALARRIEDGRNDTVRAIASCPTTIADLLATADAVASGATPIEEFV 66

Query: 987  DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD---------LSTEQLEKLKYESLIKF 1037
             GLID      + V+  +  + +   +      D          ++   E LK + L KF
Sbjct: 67   AGLIDPTAMETDDVVAISDESIDGDPVFRGEPCDECENSGEPAPASPHNETLKRDVLEKF 126

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + ++  F+ +R A+E +GY SE Y  A   I  E++ IRFT ++IE+LC  LR   +++ 
Sbjct: 127  ARVADWFEHLRDAYESDGYGSERYRTAQFAIEAELMTIRFTVRTIERLCGALRVSADELR 186

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
             IE++I  IVV++CG+PR  F+  F  NE N  W+       H ++  L RN+P+I   Q
Sbjct: 187  TIEREIARIVVDRCGVPRDAFVAEFRGNETNPAWLHQLIAAAHPFSPSLERNLPAIWLQQ 246

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            +K++ LQ  +VLPL++ R + R M   E K   AK EM EANLRLVISIAK+YT+RGL F
Sbjct: 247  EKMLVLQKRVVLPLDEFRSVCRAMATSERKTLHAKGEMIEANLRLVISIAKRYTNRGLLF 306

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLM+AVDKFE+RRGYKFSTYATWWIRQA++RS+ADQARTIRIPVHMIE+IN
Sbjct: 307  LDLIQEGNIGLMRAVDKFEFRRGYKFSTYATWWIRQAVSRSVADQARTIRIPVHMIESIN 366

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K+ RISRQILQETG EPD +V+A +M + E+KIR + ++ KEPVS++ PVG+++D+ +GD
Sbjct: 367  KLKRISRQILQETGREPDATVLAERMAVQEDKIRAMQRMIKEPVSLDMPVGENDDTSVGD 426

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
              ED   + P ++AL+ASMR  V + L +LTP E+K+LR+RFGIE +++ TLEE+G QF+
Sbjct: 427  MFEDPAAILPDESALHASMRDAVSEALTTLTPCEAKILRLRFGIEGNTECTLEELGNQFE 486

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIF 1426
            VTRERIRQIEA+ALRKLRHP R  +L+ F
Sbjct: 487  VTRERIRQIEARALRKLRHPDRSRRLRSF 515



 Score =  522 bits (1344), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 256/498 (51%), Positives = 349/498 (70%), Gaps = 9/498 (1%)

Query: 137 REMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 196
           REMG+ ELLTR GE+ +A+RIE+G  D + AI+SCPTTI ++L  AD ++     I+E V
Sbjct: 7   REMGATELLTRQGEVALARRIEDGRNDTVRAIASCPTTIADLLATADAVASGATPIEEFV 66

Query: 197 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSAD---------LSTEQLEKLKYESLIKF 247
            GLID      + V+  +  + +   +      D          ++   E LK + L KF
Sbjct: 67  AGLIDPTAMETDDVVAISDESIDGDPVFRGEPCDECENSGEPAPASPHNETLKRDVLEKF 126

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           + ++  F+ +R A+E +GY SE Y  A   I  E++ IRFT ++IE+LC  LR   +++ 
Sbjct: 127 ARVADWFEHLRDAYESDGYGSERYRTAQFAIEAELMTIRFTVRTIERLCGALRVSADELR 186

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
            IE++I  IVV++CG+PR  F+  F  NE N  W+       H ++  L RN+P+I   Q
Sbjct: 187 TIEREIARIVVDRCGVPRDAFVAEFRGNETNPAWLHQLIAAAHPFSPSLERNLPAIWLQQ 246

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           +K++ LQ  +VLPL++ R + R M   E K   AK EM EANLRLVISIAK+YT+RGL F
Sbjct: 247 EKMLVLQKRVVLPLDEFRSVCRAMATSERKTLHAKGEMIEANLRLVISIAKRYTNRGLLF 306

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLM+AVDKFE+RRGYKFSTYATWWIRQA++RS+ADQARTIRIPVHMIE+IN
Sbjct: 307 LDLIQEGNIGLMRAVDKFEFRRGYKFSTYATWWIRQAVSRSVADQARTIRIPVHMIESIN 366

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K+ RISRQILQETG EPD +V+A +M + E+KIR + ++ KEPVS++ PVG+++D+ +GD
Sbjct: 367 KLKRISRQILQETGREPDATVLAERMAVQEDKIRAMQRMIKEPVSLDMPVGENDDTSVGD 426

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
             ED   + P ++AL+ASMR  V + L +LTP E+K+LR+RFGIE +++ TLEE+G QF+
Sbjct: 427 MFEDPAAILPDESALHASMRDAVSEALTTLTPCEAKILRLRFGIEGNTECTLEELGNQFE 486

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEA+ALRKLR
Sbjct: 487 VTRERIRQIEARALRKLR 504


>gi|84394590|ref|ZP_00993293.1| RNA polymerase sigma factor, partial [Vibrio splendidus 12B01]
 gi|84374781|gb|EAP91725.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 573

 Score =  533 bits (1372), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 278/528 (52%), Positives = 366/528 (69%), Gaps = 7/528 (1%)

Query: 908  LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 967
            LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P TI  
Sbjct: 45   LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINTVQLSVAEYPGTIPY 104

Query: 968  ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 1027
            IL   D++   EI++ ++++G +D +          +  +   K  +E    + + +  E
Sbjct: 105  ILEQFDRVLAEEIRLTDLINGFVDPDDDGTAAPTATHIGSELAKTDLEDEDKEEAEDDEE 164

Query: 1028 KLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
            + + ++ I       KF+ +   +   + A  + G+ S     A   + +     R T K
Sbjct: 165  EEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHESPKATLATTMMQDVFKEFRLTPK 224

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 1140
              + L + LR  +++V   E+ I+   V    MP+  FI +F  NE +  W+D       
Sbjct: 225  QFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDK 284

Query: 1141 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 1200
             Y   + RN   I+   QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANL
Sbjct: 285  PYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANL 344

Query: 1201 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 1260
            RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 345  RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 404

Query: 1261 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 1320
            DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP
Sbjct: 405  DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 464

Query: 1321 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 1380
            +SME+P+GDDEDSHLGDFIED  +  P D+A   S+R   KD+L  LTPRE+KVLRMRFG
Sbjct: 465  ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFG 524

Query: 1381 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 525  IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 572



 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 271/515 (52%), Positives = 357/515 (69%), Gaps = 7/515 (1%)

Query: 118 LSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIME 177
           LS+V+S+ GRT DP++MYMREMG+VELLTR+GEI+IAKRIE+G+  +  +++  P TI  
Sbjct: 45  LSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINTVQLSVAEYPGTIPY 104

Query: 178 ILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE 237
           IL   D++   EI++ ++++G +D +          +  +   K  +E    + + +  E
Sbjct: 105 ILEQFDRVLAEEIRLTDLINGFVDPDDDGTAAPTATHIGSELAKTDLEDEDKEEAEDDEE 164

Query: 238 KLKYESLI-------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
           + + ++ I       KF+ +   +   + A  + G+ S     A   + +     R T K
Sbjct: 165 EEEEDTGIDPELALEKFTALRTSYQNRQLAINEYGHESPKATLATTMMQDVFKEFRLTPK 224

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
             + L + LR  +++V   E+ I+   V    MP+  FI +F  NE +  W+D       
Sbjct: 225 QFDYLVNELRTSMDRVRTQERLIMRQTVEYGKMPKKSFIALFTGNESSEAWLDEVLASDK 284

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            Y   + RN   I+   QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANL
Sbjct: 285 PYAEKIKRNEHDIRRSIQKLDIIERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANL 344

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 345 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 404

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP
Sbjct: 405 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 464

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDDEDSHLGDFIED  +  P D+A   S+R   KD+L  LTPRE+KVLRMRFG
Sbjct: 465 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFG 524

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 525 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 559


>gi|334144444|ref|YP_004537600.1| RNA polymerase sigma-70 subunit RpoD [Thioalkalimicrobium cyclicum
            ALM1]
 gi|333965355|gb|AEG32121.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalimicrobium cyclicum
            ALM1]
          Length = 595

 Score =  529 bits (1363), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 294/603 (48%), Positives = 403/603 (66%), Gaps = 30/603 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI+  K+ GYLT++++ND LP+DI + + +  ++       I + +   + + L+     
Sbjct: 13   LIERAKDLGYLTYADVNDVLPDDI-EEDQLSQVLTILGDFGIPLFDTAPEEDELITKEGG 71

Query: 896  S-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            + D+   EA   AL+ VDS+FGRT DP++MYMREMGSVELLTR GEI+IAKRIE  ++DM
Sbjct: 72   AFDEAAAEAAILALAEVDSEFGRTTDPVRMYMREMGSVELLTRKGEIDIAKRIESNIRDM 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEE-- 1010
            + ++S  P    +IL A  K+   E K+ +++ G ID N   + +V  +  + +NN E  
Sbjct: 132  LDSLSKYPMCAEKILRAFQKMDDGEGKLADVIQGFIDPNDLEDVQVEDLSADSDNNSEPK 191

Query: 1011 -----KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
                 + LI++  ADL     EKL  +++              KA +  G +     K  
Sbjct: 192  DDSIDQALIDAFLADL-----EKLHRDAV--------------KAEDLHGSSDPKAKKKR 232

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              + + +  ++        +   ++ +I+Q+ + E+ I+  VV    +PR  F+++F  N
Sbjct: 233  QLVVDHLRTVKLVPLFTNGVIRDIKIKISQIREQERVIVNAVVRNVKIPRTRFVELFVGN 292

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E +  +VD       D   +L      +K  Q++L  ++    + ++  + + + +   E
Sbjct: 293  ETSPEFVDMLIGEYTDKTDLLEEVRQDVKRAQKRLALIEKSEKMAISYYKKVYKDLSKSE 352

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 353  SQARAAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 412

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEM
Sbjct: 413  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEM 472

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK+MKIAKEP+SME+P+GDDEDS LGDFIED N+L+PSD+A    M   V+++L+
Sbjct: 473  PEDKIRKVMKIAKEPISMETPIGDDEDSSLGDFIEDSNILSPSDSADLEGMSETVREMLS 532

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
            +LTPRE+KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ 
Sbjct: 533  TLTPREAKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAERLRS 592

Query: 1426 FLE 1428
            FL+
Sbjct: 593  FLD 595



 Score =  513 bits (1321), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 287/590 (48%), Positives = 393/590 (66%), Gaps = 30/590 (5%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI+  K+ GYLT++++ND LP+DI + + +  ++       I + +   + + L+     
Sbjct: 13  LIERAKDLGYLTYADVNDVLPDDI-EEDQLSQVLTILGDFGIPLFDTAPEEDELITKEGG 71

Query: 106 S-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           + D+   EA   AL+ VDS+FGRT DP++MYMREMGSVELLTR GEI+IAKRIE  ++DM
Sbjct: 72  AFDEAAAEAAILALAEVDSEFGRTTDPVRMYMREMGSVELLTRKGEIDIAKRIESNIRDM 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEE-- 220
           + ++S  P    +IL A  K+   E K+ +++ G ID N   + +V  +  + +NN E  
Sbjct: 132 LDSLSKYPMCAEKILRAFQKMDDGEGKLADVIQGFIDPNDLEDVQVEDLSADSDNNSEPK 191

Query: 221 -----KILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
                + LI++  ADL     EKL  +++              KA +  G +     K  
Sbjct: 192 DDSIDQALIDAFLADL-----EKLHRDAV--------------KAEDLHGSSDPKAKKKR 232

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             + + +  ++        +   ++ +I+Q+ + E+ I+  VV    +PR  F+++F  N
Sbjct: 233 QLVVDHLRTVKLVPLFTNGVIRDIKIKISQIREQERVIVNAVVRNVKIPRTRFVELFVGN 292

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E +  +VD       D   +L      +K  Q++L  ++    + ++  + + + +   E
Sbjct: 293 ETSPEFVDMLIGEYTDKTDLLEEVRQDVKRAQKRLALIEKSEKMAISYYKKVYKDLSKSE 352

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 353 SQARAAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 412

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEM
Sbjct: 413 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEM 472

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK+MKIAKEP+SME+P+GDDEDS LGDFIED N+L+PSD+A    M   V+++L+
Sbjct: 473 PEDKIRKVMKIAKEPISMETPIGDDEDSSLGDFIEDSNILSPSDSADLEGMSETVREMLS 532

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +LTPRE+KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 533 TLTPREAKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 582


>gi|350564682|ref|ZP_08933499.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalimicrobium
            aerophilum AL3]
 gi|349777701|gb|EGZ32064.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalimicrobium
            aerophilum AL3]
          Length = 595

 Score =  527 bits (1357), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 293/603 (48%), Positives = 399/603 (66%), Gaps = 30/603 (4%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI+  K+ GYLT++++ND LP+DI + + +  ++       I + +   + + L+     
Sbjct: 13   LIERAKDLGYLTYADVNDVLPDDI-EEDQLSQVLTILGDFGIPLFDTAPEEDELITKEGG 71

Query: 896  S-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
            + D+   EA   AL+ VDS+FGRT DP++MYMREMGSVELLTR GEI+IAKRIE  ++DM
Sbjct: 72   AFDEAAAEAAILALAEVDSEFGRTTDPVRMYMREMGSVELLTRKGEIDIAKRIESNIRDM 131

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEK- 1011
            + ++S  P    +IL A  K+   E K+ +++ G ID N      V  +  + +NN E  
Sbjct: 132  LDSLSKYPMCAEKILKAFQKMDDGEGKLADVIQGFIDPNDLEEVEVEDLNADSDNNAEPK 191

Query: 1012 ------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 1065
                   LIE+  A     +LEKL  +++              KA +  G +     +  
Sbjct: 192  DDSIDPALIEAFLA-----ELEKLHRDAV--------------KAEDTHGSSDPKAKQKR 232

Query: 1066 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 1125
              + + +  ++        +   ++ +I  + + E+ I+  VV K  +PR  F+++F +N
Sbjct: 233  QLVVDHLRTVKLVPLFTNGVIRDIKGKIAAIREQERVIVNAVVRKVKIPRTRFVELFVDN 292

Query: 1126 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 1185
            E N   +D       D   +L      +K  Q++L  ++    + ++  + + + +   E
Sbjct: 293  EANPQLIDMLIAEYPDKAGLLDEVRLDVKRAQKRLALIEKSEKMAISYYKKVYKDLSKSE 352

Query: 1186 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245
             +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 353  SQARAAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 412

Query: 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 1305
            YATWWIRQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEM
Sbjct: 413  YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEM 472

Query: 1306 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 1365
            PE+KIRK+MKIAKEP+SME+P+GDDEDS LGDFIED N+L+PSD+A    M   V+++L+
Sbjct: 473  PEDKIRKVMKIAKEPISMETPIGDDEDSSLGDFIEDSNILSPSDSADLEGMSETVREMLS 532

Query: 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425
            +LTPRE+KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  +L+ 
Sbjct: 533  TLTPREAKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAERLRS 592

Query: 1426 FLE 1428
            FL+
Sbjct: 593  FLD 595



 Score =  511 bits (1315), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 286/590 (48%), Positives = 389/590 (65%), Gaps = 30/590 (5%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI+  K+ GYLT++++ND LP+DI + + +  ++       I + +   + + L+     
Sbjct: 13  LIERAKDLGYLTYADVNDVLPDDI-EEDQLSQVLTILGDFGIPLFDTAPEEDELITKEGG 71

Query: 106 S-DDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
           + D+   EA   AL+ VDS+FGRT DP++MYMREMGSVELLTR GEI+IAKRIE  ++DM
Sbjct: 72  AFDEAAAEAAILALAEVDSEFGRTTDPVRMYMREMGSVELLTRKGEIDIAKRIESNIRDM 131

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEK- 221
           + ++S  P    +IL A  K+   E K+ +++ G ID N      V  +  + +NN E  
Sbjct: 132 LDSLSKYPMCAEKILKAFQKMDDGEGKLADVIQGFIDPNDLEEVEVEDLNADSDNNAEPK 191

Query: 222 ------ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAH 275
                  LIE+  A     +LEKL  +++              KA +  G +     +  
Sbjct: 192 DDSIDPALIEAFLA-----ELEKLHRDAV--------------KAEDTHGSSDPKAKQKR 232

Query: 276 NNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPEN 335
             + + +  ++        +   ++ +I  + + E+ I+  VV K  +PR  F+++F +N
Sbjct: 233 QLVVDHLRTVKLVPLFTNGVIRDIKGKIAAIREQERVIVNAVVRKVKIPRTRFVELFVDN 292

Query: 336 EINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGE 395
           E N   +D       D   +L      +K  Q++L  ++    + ++  + + + +   E
Sbjct: 293 EANPQLIDMLIAEYPDKAGLLDEVRLDVKRAQKRLALIEKSEKMAISYYKKVYKDLSKSE 352

Query: 396 MKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455
            +AR AKREM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST
Sbjct: 353 SQARAAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 412

Query: 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEM 515
           YATWWIRQAITRSIADQARTIRIPVHMIETINK++RI RQ+LQ+ G EP P  +A +MEM
Sbjct: 413 YATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIQRQLLQKMGREPTPEELAEEMEM 472

Query: 516 PEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILN 575
           PE+KIRK+MKIAKEP+SME+P+GDDEDS LGDFIED N+L+PSD+A    M   V+++L+
Sbjct: 473 PEDKIRKVMKIAKEPISMETPIGDDEDSSLGDFIEDSNILSPSDSADLEGMSETVREMLS 532

Query: 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +LTPRE+KVLRMRFG+ M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 533 TLTPREAKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 582


>gi|269468904|gb|EEZ80491.1| DNA-directed RNA polymerase, sigma subunit [uncultured SUP05 cluster
            bacterium]
          Length = 603

 Score =  523 bits (1348), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 284/615 (46%), Positives = 411/615 (66%), Gaps = 16/615 (2%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +K+ ++   + L+K    LI +GKE+GYLT++EIND LPED++  E +E I+     +DI
Sbjct: 1    MKTTTKAHKQALQK----LIMIGKEQGYLTYAEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 878  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 936
            +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57   AVSDTVPDADTLVVESGAKAQSTSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 937  RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 994
            +  EI IAK IE G+ +++ +I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117  QSDEIRIAKEIEAGVFEIMKSITLYPAITGFFFKAHTRLEEGKCKMTDVIIGYQGDAEDF 176

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHFDKMRKAFEK 1053
            +         + +++E+            ++ +   ++E+++K S      +  +K  EK
Sbjct: 177  AKKKAAFDAGEFDDDEEYEEMEEMEYTGPDEGQVYGRFETVLKCS------EAYQKTNEK 230

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G+  +  I A   +S  +  +R   K +  + + + +++  V + EK I    +   GM
Sbjct: 231  HGFRDKKTIAARQQLSEGLSDLRLAPKLVSTMMEVICDRVALVKKQEKTIQSACLY-AGM 289

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
             R  F K+F +NE N +W+    K+       L  +   I   Q+ L+  + ++ L + +
Sbjct: 290  EREQFFKLFNDNETNFDWLKG-AKLDKKVAEALKVSKDEIYYAQKNLLEFEEEMQLTVPE 348

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVD
Sbjct: 349  LKALNKLYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVD 408

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E
Sbjct: 409  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGRE 468

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
              P  +A++ME+PE KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N+ +P +    
Sbjct: 469  ATPEELAVEMELPEYKINKILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTR 528

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S++    ++L +L+PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRK
Sbjct: 529  ESLKETTGELLANLSPREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRK 588

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR +KL+ FLE
Sbjct: 589  LRHPSRAHKLQSFLE 603



 Score =  504 bits (1297), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 275/602 (45%), Positives = 400/602 (66%), Gaps = 16/602 (2%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           +K+ ++   + L+K    LI +GKE+GYLT++EIND LPED++  E +E I+     +DI
Sbjct: 1   MKTTTKAHKQALQK----LIMIGKEQGYLTYAEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 88  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 146
           +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57  AVSDTVPDADTLVVESGAKAQSTSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 147 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 204
           +  EI IAK IE G+ +++ +I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117 QSDEIRIAKEIEAGVFEIMKSITLYPAITGFFFKAHTRLEEGKCKMTDVIIGYQGDAEDF 176

Query: 205 SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHFDKMRKAFEK 263
           +         + +++E+            ++ +   ++E+++K S      +  +K  EK
Sbjct: 177 AKKKAAFDAGEFDDDEEYEEMEEMEYTGPDEGQVYGRFETVLKCS------EAYQKTNEK 230

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G+  +  I A   +S  +  +R   K +  + + + +++  V + EK I    +   GM
Sbjct: 231 HGFRDKKTIAARQQLSEGLSDLRLAPKLVSTMMEVICDRVALVKKQEKTIQSACLY-AGM 289

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
            R  F K+F +NE N +W+    K+       L  +   I   Q+ L+  + ++ L + +
Sbjct: 290 EREQFFKLFNDNETNFDWLKG-AKLDKKVAEALKVSKDEIYYAQKNLLEFEEEMQLTVPE 348

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVD
Sbjct: 349 LKALNKLYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVD 408

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E
Sbjct: 409 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGRE 468

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
             P  +A++ME+PE KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N+ +P +    
Sbjct: 469 ATPEELAVEMELPEYKINKILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTR 528

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S++    ++L +L+PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRK
Sbjct: 529 ESLKETTGELLANLSPREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRK 588

Query: 624 LR 625
           LR
Sbjct: 589 LR 590


>gi|424864416|ref|ZP_18288320.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86B]
 gi|400759845|gb|EJP74026.1| RNA polymerase sigma factor RpoD [SAR86 cluster bacterium SAR86B]
          Length = 576

 Score =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 273/570 (47%), Positives = 384/570 (67%), Gaps = 11/570 (1%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
           LI  G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D + LMLS   
Sbjct: 14  LISKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADELMLSESE 73

Query: 106 SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
             DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++++
Sbjct: 74  DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMREL 133

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 224
           ++A    P T+   +     +   E KI++ + G +++          G +   +E+   
Sbjct: 134 LNASVYYPNTVEYAMEFFQLVKDEEKKINDFITGFLEE-MEEVPSAGPGTERAKQEEESD 192

Query: 225 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 284
           +  S  L  +++++       + +N+   ++K +K  E +G NS+   K    +      
Sbjct: 193 DEDSGGLDIKEVQR-------RMTNLKRQYNKTQKVIESKGRNSKEAQKEFEKLGQIFQF 245

Query: 285 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 344
           ++F+ +  + L    RN ++ + + E+ I   +V K  MPR  F+ +FPEN   + W+D+
Sbjct: 246 LKFSPRMFDDLSIIARNGLSAIREKERFIQLQLVKKARMPRKDFLALFPENVTKVRWIDS 305

Query: 345 ETKIQHDYNLILCRNIPSIKELQQK-LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
             K +  Y   L + +     + QK +I+++  + L + +++DINRKM  GE K R+AK+
Sbjct: 306 LMK-EKKYKKDLLQAVKQDVVIAQKDIIDIEKRVGLSIKEIKDINRKMSMGETKMRRAKK 364

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           +M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 365 DMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 424

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK+
Sbjct: 425 AITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKV 484

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           +KIAKEP+S E+P+GDDEDS LGDFIED  + +P D A   S+     DIL SLT RE+K
Sbjct: 485 LKIAKEPISTETPIGDDEDSSLGDFIEDTVIDSPVDVATEDSLHFATDDILGSLTAREAK 544

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613
           VLRMRFGI M++DHTLEEVGKQFDVTRERI
Sbjct: 545 VLRMRFGIGMNTDHTLEEVGKQFDVTRERI 574



 Score =  521 bits (1343), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 273/570 (47%), Positives = 384/570 (67%), Gaps = 11/570 (1%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
            LI  G+E+GYLT++++ND LPEDI D + ++ II     + + V E   D + LMLS   
Sbjct: 14   LISKGREQGYLTYADVNDHLPEDISDPDQVDEIIGMINDLGLQVHETAPDADELMLSESE 73

Query: 896  SDDDVEEATEAALST-VDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
              DD+     A     V+++ GRT DP++MYMREMG+V+LLTR+GEIEIAKRIEEG++++
Sbjct: 74   DSDDIALEQAAEALAAVENETGRTTDPVRMYMREMGTVDLLTREGEIEIAKRIEEGMREL 133

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILI 1014
            ++A    P T+   +     +   E KI++ + G +++          G +   +E+   
Sbjct: 134  LNASVYYPNTVEYAMEFFQLVKDEEKKINDFITGFLEE-MEEVPSAGPGTERAKQEEESD 192

Query: 1015 ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLG 1074
            +  S  L  +++++       + +N+   ++K +K  E +G NS+   K    +      
Sbjct: 193  DEDSGGLDIKEVQR-------RMTNLKRQYNKTQKVIESKGRNSKEAQKEFEKLGQIFQF 245

Query: 1075 IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 1134
            ++F+ +  + L    RN ++ + + E+ I   +V K  MPR  F+ +FPEN   + W+D+
Sbjct: 246  LKFSPRMFDDLSIIARNGLSAIREKERFIQLQLVKKARMPRKDFLALFPENVTKVRWIDS 305

Query: 1135 ETKIQHDYNLILCRNIPSIKELQQK-LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
              K +  Y   L + +     + QK +I+++  + L + +++DINRKM  GE K R+AK+
Sbjct: 306  LMK-EKKYKKDLLQAVKQDVVIAQKDIIDIEKRVGLSIKEIKDINRKMSMGETKMRRAKK 364

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            +M EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 365  DMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 424

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++R+SRQ++Q+ G EP P  ++ +++MPE+K+RK+
Sbjct: 425  AITRSIADQARTIRIPVHMIETINKLNRVSRQMMQDMGREPTPEELSKELDMPEDKVRKV 484

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+S E+P+GDDEDS LGDFIED  + +P D A   S+     DIL SLT RE+K
Sbjct: 485  LKIAKEPISTETPIGDDEDSSLGDFIEDTVIDSPVDVATEDSLHFATDDILGSLTAREAK 544

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERI 1403
            VLRMRFGI M++DHTLEEVGKQFDVTRERI
Sbjct: 545  VLRMRFGIGMNTDHTLEEVGKQFDVTRERI 574


>gi|126642737|ref|YP_001085721.1| sigma D (sigma 70) factor of RNA polymerase major sigma factor during
            exponential growth [Acinetobacter baumannii ATCC 17978]
          Length = 580

 Score =  521 bits (1342), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 273/572 (47%), Positives = 383/572 (66%), Gaps = 20/572 (3%)

Query: 877  ISVSEHVLDTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 934
            I V E   +++  M   S   +D+  EE   A L++V+++ GRT DP++MYMREMG+VEL
Sbjct: 7    IPVHERAPESDDTMFGESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVEL 66

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 994
            LTR+GEI IAKRIEEG++D++++I+  P  +  +L   +     E ++ +I+ G +D   
Sbjct: 67   LTREGEISIAKRIEEGIRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPET 126

Query: 995  SSN------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKF 1037
              +                   K+  E K+  +    +   +   +         + ++F
Sbjct: 127  DEDIPEVLEDVEELEEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRF 186

Query: 1038 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 1097
            + +   + + +   EK G NS    +A  +++   +  +FT +  + + + +R    Q+ 
Sbjct: 187  AELEAAWAQTKAVIEKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIR 246

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKEL 1156
              E++I+   V +  M R  F   FP+ E N  W+D +  K   +    L +  P +   
Sbjct: 247  ANEREIMRYAVRRGRMDRNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAF 306

Query: 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 1216
            QQK+ +++ ++ L +++++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 307  QQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 366

Query: 1217 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276
            FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 367  FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 426

Query: 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336
            NKI+R+SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 427  NKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLG 486

Query: 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396
            DFIED+N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQF
Sbjct: 487  DFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQF 546

Query: 1397 DVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DVTRERIRQIEAKALRKLRHPSR   L+ FLE
Sbjct: 547  DVTRERIRQIEAKALRKLRHPSRSEHLRSFLE 578



 Score =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 265/559 (47%), Positives = 374/559 (66%), Gaps = 20/559 (3%)

Query: 87  ISVSEHVLDTETLML--SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVEL 144
           I V E   +++  M   S   +D+  EE   A L++V+++ GRT DP++MYMREMG+VEL
Sbjct: 7   IPVHERAPESDDTMFGESADATDEVAEEEAAAVLASVENEPGRTTDPVRMYMREMGTVEL 66

Query: 145 LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNF 204
           LTR+GEI IAKRIEEG++D++++I+  P  +  +L   +     E ++ +I+ G +D   
Sbjct: 67  LTREGEISIAKRIEEGIRDVLNSIAYWPNAVEVVLKEYNDFLTGERRLADILSGYLDPET 126

Query: 205 SSN------------NRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYE-----SLIKF 247
             +                   K+  E K+  +    +   +   +         + ++F
Sbjct: 127 DEDIPEVLEDVEELEEEDESSTKSTKEVKLDDDDEEEESEGDDDSEGDSGPDPEVAKVRF 186

Query: 248 SNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVT 307
           + +   + + +   EK G NS    +A  +++   +  +FT +  + + + +R    Q+ 
Sbjct: 187 AELEAAWAQTKAVIEKHGRNSPEANEALESLATVFMMFKFTPRLFDIISEMIRGTHEQIR 246

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE-TKIQHDYNLILCRNIPSIKEL 366
             E++I+   V +  M R  F   FP+ E N  W+D +  K   +    L +  P +   
Sbjct: 247 ANEREIMRYAVRRGRMDRNQFRTSFPKQESNPAWLDEQIAKAPAEIKAHLEKVRPDVLAF 306

Query: 367 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQ 426
           QQK+ +++ ++ L +++++DI+++M  GE KAR+AK+EM EANLRLVISIAKKYT+RGLQ
Sbjct: 307 QQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQ 366

Query: 427 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486
           FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI
Sbjct: 367 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 426

Query: 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546
           NKI+R+SRQ+LQE G EP P  +  ++EM E K+RK++KIAKEP+SME+P+GDDEDSHLG
Sbjct: 427 NKINRVSRQLLQEMGREPTPEELGERLEMDEVKVRKVLKIAKEPISMETPIGDDEDSHLG 486

Query: 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 606
           DFIED+N+ +P DAA +  ++   +++L +LT RE+KVL+MRFGI+M +DHTLEEVGKQF
Sbjct: 487 DFIEDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQF 546

Query: 607 DVTRERIRQIEAKALRKLR 625
           DVTRERIRQIEAKALRKLR
Sbjct: 547 DVTRERIRQIEAKALRKLR 565


>gi|148244277|ref|YP_001218971.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
            Vesicomyosocius okutanii HA]
 gi|146326104|dbj|BAF61247.1| DNA-directed RNA polymerase sigma-70 factor [Candidatus
            Vesicomyosocius okutanii HA]
          Length = 603

 Score =  519 bits (1336), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 291/615 (47%), Positives = 415/615 (67%), Gaps = 16/615 (2%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +KS ++   + L+K    LI +GKE+GYLT+SEIND LPED++  E +E I+     +DI
Sbjct: 1    MKSTTKAHKQALQK----LIMVGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 878  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 936
            +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57   TVSDTVPDADTLVVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 937  RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 994
            ++ EI IAK IE G+ +++ +I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117  QEDEIRIAKEIEAGVFEIMQSITLYPVITDFFFKAHTRLEEGKCKMTDVIIGYQGDAEDF 176

Query: 995  SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHFDKMRKAFEK 1053
            ++        + +N+E+            ++ +   ++++++K+S          K  E+
Sbjct: 177  ANKKVAFDAGEFDNDEEYEEIEEMEYTGPDKNQVYNRFDTVLKYSKT------YNKTTEQ 230

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113
             G+  +  IK    +S  +  +R   K +  + + + N+++QV + EK I  I ++  G+
Sbjct: 231  LGFRHKKTIKTRQQLSKGLSDLRLAPKLVNTMIEVICNRVSQVKEQEKIIKNICLD-AGI 289

Query: 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 1173
             RLHF ++F  NE N NW+D   K+       L  +   I   Q+ L   + ++ L + +
Sbjct: 290  NRLHFFELFSNNETNFNWLDT-VKLDEKIEKNLKDSKDKIYYAQKNLQQFEEEMQLTIVE 348

Query: 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 1233
            L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVD
Sbjct: 349  LKKLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVD 408

Query: 1234 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 1293
            KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E
Sbjct: 409  KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGRE 468

Query: 1294 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353
                 +A +ME+PE KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N+ +P +    
Sbjct: 469  ASSEELATEMELPEYKIIKILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTK 528

Query: 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413
             S+R    D+L++L+PRE+KVL+MRFGI M++DHTLEEVG+QFDVTRERIRQIEAKALRK
Sbjct: 529  ESLRETTGDLLSNLSPREAKVLKMRFGINMNTDHTLEEVGRQFDVTRERIRQIEAKALRK 588

Query: 1414 LRHPSRYYKLKIFLE 1428
            LRHPSR +KL+ FLE
Sbjct: 589  LRHPSRAHKLQSFLE 603



 Score =  499 bits (1285), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 282/602 (46%), Positives = 404/602 (67%), Gaps = 16/602 (2%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           +KS ++   + L+K    LI +GKE+GYLT+SEIND LPED++  E +E I+     +DI
Sbjct: 1   MKSTTKAHKQALQK----LIMVGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 88  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 146
           +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57  TVSDTVPDADTLVVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 147 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 204
           ++ EI IAK IE G+ +++ +I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117 QEDEIRIAKEIEAGVFEIMQSITLYPVITDFFFKAHTRLEEGKCKMTDVIIGYQGDAEDF 176

Query: 205 SSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKL-KYESLIKFSNISFHFDKMRKAFEK 263
           ++        + +N+E+            ++ +   ++++++K+S          K  E+
Sbjct: 177 ANKKVAFDAGEFDNDEEYEEIEEMEYTGPDKNQVYNRFDTVLKYSKT------YNKTTEQ 230

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323
            G+  +  IK    +S  +  +R   K +  + + + N+++QV + EK I  I ++  G+
Sbjct: 231 LGFRHKKTIKTRQQLSKGLSDLRLAPKLVNTMIEVICNRVSQVKEQEKIIKNICLD-AGI 289

Query: 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLND 383
            RLHF ++F  NE N NW+D   K+       L  +   I   Q+ L   + ++ L + +
Sbjct: 290 NRLHFFELFSNNETNFNWLDT-VKLDEKIEKNLKDSKDKIYYAQKNLQQFEEEMQLTIVE 348

Query: 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVD 443
           L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVD
Sbjct: 349 LKKLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVD 408

Query: 444 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSE 503
           KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E
Sbjct: 409 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGRE 468

Query: 504 PDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563
                +A +ME+PE KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N+ +P +    
Sbjct: 469 ASSEELATEMELPEYKIIKILKIAKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEITTK 528

Query: 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623
            S+R    D+L++L+PRE+KVL+MRFGI M++DHTLEEVG+QFDVTRERIRQIEAKALRK
Sbjct: 529 ESLRETTGDLLSNLSPREAKVLKMRFGINMNTDHTLEEVGRQFDVTRERIRQIEAKALRK 588

Query: 624 LR 625
           LR
Sbjct: 589 LR 590


>gi|118602160|ref|YP_903375.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
            str. Cm (Calyptogena magnifica)]
 gi|118567099|gb|ABL01904.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Ruthia magnifica
            str. Cm (Calyptogena magnifica)]
          Length = 600

 Score =  518 bits (1333), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 296/618 (47%), Positives = 412/618 (66%), Gaps = 25/618 (4%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +KS ++   ++L+K    LI  GKE+GYLT+SEIND LPED++  E +E I+     +DI
Sbjct: 1    MKSTTKAHKQSLQK----LIMAGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 878  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 936
            +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57   AVSDIVPDADTLVVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 937  RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 994
            ++ EI IAK IE G+ +++  I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117  QEDEIRIAKEIEAGVFEIMKGITLYPVITDFFFKAHTRLEEGKCKMTDVIIGYQGDTEDF 176

Query: 995  SSNNRVIKGNK-NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 1053
            +         K +N+EE   +E +  D      E   Y    +F  IS       +  EK
Sbjct: 177  AVKKAAFDAGKFDNDEEHEDMEYTGPD------ENQVYN---RFETISKCSKTYNETNEK 227

Query: 1054 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC-- 1111
             G+  +  I+    +S  +  +R   K +  + + + N++ QV + EK I     NKC  
Sbjct: 228  LGFRHKKTIEMRQQLSQSLSDLRLAPKLVNTMIEVICNRVEQVKKQEKTIQ----NKCLD 283

Query: 1112 -GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 1170
             GM RL+F + F +NE N +W+ +  K+       L  +   I   Q+ L   + ++ L 
Sbjct: 284  AGMNRLYFFESFSKNETNFDWL-SAIKLDEKTEEKLKVSKDEIYYAQKNLQQFEEEMQLT 342

Query: 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230
            + +L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMK
Sbjct: 343  ITELKTLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMK 402

Query: 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 1290
            AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ 
Sbjct: 403  AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKF 462

Query: 1291 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350
            G E  P  +A +ME+PE KI KI+KI+KEP+SME+PVGDDEDS++GDFIED N+ +P + 
Sbjct: 463  GREASPEELATEMELPEYKIIKILKISKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEI 522

Query: 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410
                S+R    ++L++L+PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKA
Sbjct: 523  TTKESLRETTSELLSNLSPREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 582

Query: 1411 LRKLRHPSRYYKLKIFLE 1428
            LRKLRHPSR +KL+ FLE
Sbjct: 583  LRKLRHPSRAHKLQSFLE 600



 Score =  498 bits (1282), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 287/605 (47%), Positives = 401/605 (66%), Gaps = 25/605 (4%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           +KS ++   ++L+K    LI  GKE+GYLT+SEIND LPED++  E +E I+     +DI
Sbjct: 1   MKSTTKAHKQSLQK----LIMAGKEKGYLTYSEINDILPEDLLTQEQVEPIVTILEELDI 56

Query: 88  SVSEHVLDTETLML-SNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 146
           +VS+ V D +TL++ S   +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL 
Sbjct: 57  AVSDIVPDADTLVVESGAKAQSTSAEAAIAALAALDSEFGRTTDPVRMYMREMGVVDLLE 116

Query: 147 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNF 204
           ++ EI IAK IE G+ +++  I+  P        A  ++ + + K+ +++ G     ++F
Sbjct: 117 QEDEIRIAKEIEAGVFEIMKGITLYPVITDFFFKAHTRLEEGKCKMTDVIIGYQGDTEDF 176

Query: 205 SSNNRVIKGNK-NNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK 263
           +         K +N+EE   +E +  D      E   Y    +F  IS       +  EK
Sbjct: 177 AVKKAAFDAGKFDNDEEHEDMEYTGPD------ENQVYN---RFETISKCSKTYNETNEK 227

Query: 264 EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC-- 321
            G+  +  I+    +S  +  +R   K +  + + + N++ QV + EK I     NKC  
Sbjct: 228 LGFRHKKTIEMRQQLSQSLSDLRLAPKLVNTMIEVICNRVEQVKKQEKTIQ----NKCLD 283

Query: 322 -GMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLP 380
            GM RL+F + F +NE N +W+ +  K+       L  +   I   Q+ L   + ++ L 
Sbjct: 284 AGMNRLYFFESFSKNETNFDWL-SAIKLDEKTEEKLKVSKDEIYYAQKNLQQFEEEMQLT 342

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           + +L+ +N+    G+ +A+KAK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMK
Sbjct: 343 ITELKTLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMK 402

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ 
Sbjct: 403 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKF 462

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G E  P  +A +ME+PE KI KI+KI+KEP+SME+PVGDDEDS++GDFIED N+ +P + 
Sbjct: 463 GREASPEELATEMELPEYKIIKILKISKEPLSMETPVGDDEDSNIGDFIEDTNLSSPVEI 522

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
               S+R    ++L++L+PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKA
Sbjct: 523 TTKESLRETTSELLSNLSPREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 582

Query: 621 LRKLR 625
           LRKLR
Sbjct: 583 LRKLR 587


>gi|117924113|ref|YP_864730.1| RpoD family RNA polymerase sigma factor [Magnetococcus marinus MC-1]
 gi|117607869|gb|ABK43324.1| RNA polymerase, sigma 70 subunit, RpoD [Magnetococcus marinus MC-1]
          Length = 683

 Score =  516 bits (1329), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 305/694 (43%), Positives = 417/694 (60%), Gaps = 93/694 (13%)

Query: 816  FDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 875
             D KSN  E+ +  R+  K LI  GKERG+LT+ E+ND LP D+   E +E ++     M
Sbjct: 1    MDGKSNMAEDTK--REDMKKLIARGKERGFLTYDEVNDVLPNDMTSAEDMEDVVGLLDNM 58

Query: 876  DISVSEHVLDTE-----------TLMLSNITS-DDDVEEA-------------------- 903
             I +    +D E              + N+ S DDDV+E                     
Sbjct: 59   GIDL----IDDEREEGARPKSRPAAGIGNLDSLDDDVDEEILGISDFDSEDDESDDEDGL 114

Query: 904  -TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCP 962
             ++ A+   D D G+T DP++MY+REMGSVELLTR+GEI IAKRIEEG  ++I  I   P
Sbjct: 115  RSDGAIE--DIDLGKTDDPVRMYLREMGSVELLTREGEIAIAKRIEEGCNEVIATICDAP 172

Query: 963  TTIMEILIAADKISKNEIKIDEIVD----------------------------------- 987
            +T  E+++ A+++   EI + E++D                                   
Sbjct: 173  STFNEVMMLAERLRAGEISLREVLDISTPQDEGSEDEDLNNDDDEVEASTESDDEDVDED 232

Query: 988  GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH---- 1043
             +++      N V +      EE+I   ++  +   EQ  +L   +L  F  I+      
Sbjct: 233  DIVNGPVKVRNPVPEPPPVKTEEEI---AAQREADNEQFRELYEATLAIFDEITRENEVL 289

Query: 1044 ---FDKMRKAFE--KEGYNSESYI---KAHN-NISNEMLGIRFTAKSIEKLCDTLRNQIN 1094
                D +  A +   EG   +  +   +AH   I   + GI+F+ K  ++L + +++ + 
Sbjct: 290  VELRDPLNDALQNDPEGETCKRLLAEYQAHKARIVEIVAGIKFSPKQRDRLVERIKSYVA 349

Query: 1095 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 1154
             V   E++I+ IV  +C + +  FI+ F  NE +  W+ N  K +      L      I 
Sbjct: 350  AVRAQEQKIITIVT-QCNVKKPEFIEQFTGNESDTTWIQNFAKTRSAPWKRLYEQSELIC 408

Query: 1155 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214
            E Q  + +++ +    + DL+  N+K++ GE +A +AK+EM EANLRLVISIAKKYT+RG
Sbjct: 409  EAQLVIRSIEEEAGQTVADLKKCNKKLMDGERRANQAKKEMVEANLRLVISIAKKYTNRG 468

Query: 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 1274
            LQFLDLIQEGNIGLMKAVDKFE+RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 469  LQFLDLIQEGNIGLMKAVDKFEWRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 528

Query: 1275 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334
            TINK+ R SRQ++QE G EP P  IA +M M  EK+RK++KIAKEP+S+E+PVGD+EDSH
Sbjct: 529  TINKLVRTSRQMVQEMGREPTPEEIAERMSMSLEKVRKVLKIAKEPISLETPVGDEEDSH 588

Query: 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 1394
            LGDFIED++ML+PS+ A+ +++R     +L +LT RE  VLRMRFGI + +DHTLEEVGK
Sbjct: 589  LGDFIEDKSMLSPSEHAIMSNLRDTTGRVLQTLTSREEHVLRMRFGIGLPTDHTLEEVGK 648

Query: 1395 QFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            QF+VTRERIRQIEAKALRKLRHP+R  KL+ FLE
Sbjct: 649  QFNVTRERIRQIEAKALRKLRHPTRSRKLRSFLE 682



 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 297/681 (43%), Positives = 407/681 (59%), Gaps = 93/681 (13%)

Query: 26  FDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYM 85
            D KSN  E+ +  R+  K LI  GKERG+LT+ E+ND LP D+   E +E ++     M
Sbjct: 1   MDGKSNMAEDTK--REDMKKLIARGKERGFLTYDEVNDVLPNDMTSAEDMEDVVGLLDNM 58

Query: 86  DISVSEHVLDTE-----------TLMLSNITS-DDDVEEA-------------------- 113
            I +    +D E              + N+ S DDDV+E                     
Sbjct: 59  GIDL----IDDEREEGARPKSRPAAGIGNLDSLDDDVDEEILGISDFDSEDDESDDEDGL 114

Query: 114 -TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCP 172
            ++ A+   D D G+T DP++MY+REMGSVELLTR+GEI IAKRIEEG  ++I  I   P
Sbjct: 115 RSDGAIE--DIDLGKTDDPVRMYLREMGSVELLTREGEIAIAKRIEEGCNEVIATICDAP 172

Query: 173 TTIMEILIAADKISKNEIKIDEIVD----------------------------------- 197
           +T  E+++ A+++   EI + E++D                                   
Sbjct: 173 STFNEVMMLAERLRAGEISLREVLDISTPQDEGSEDEDLNNDDDEVEASTESDDEDVDED 232

Query: 198 GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFH---- 253
            +++      N V +      EE+I   ++  +   EQ  +L   +L  F  I+      
Sbjct: 233 DIVNGPVKVRNPVPEPPPVKTEEEI---AAQREADNEQFRELYEATLAIFDEITRENEVL 289

Query: 254 ---FDKMRKAFE--KEGYNSESYI---KAHN-NISNEMLGIRFTAKSIEKLCDTLRNQIN 304
               D +  A +   EG   +  +   +AH   I   + GI+F+ K  ++L + +++ + 
Sbjct: 290 VELRDPLNDALQNDPEGETCKRLLAEYQAHKARIVEIVAGIKFSPKQRDRLVERIKSYVA 349

Query: 305 QVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIK 364
            V   E++I+ IV  +C + +  FI+ F  NE +  W+ N  K +      L      I 
Sbjct: 350 AVRAQEQKIITIVT-QCNVKKPEFIEQFTGNESDTTWIQNFAKTRSAPWKRLYEQSELIC 408

Query: 365 ELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 424
           E Q  + +++ +    + DL+  N+K++ GE +A +AK+EM EANLRLVISIAKKYT+RG
Sbjct: 409 EAQLVIRSIEEEAGQTVADLKKCNKKLMDGERRANQAKKEMVEANLRLVISIAKKYTNRG 468

Query: 425 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 484
           LQFLDLIQEGNIGLMKAVDKFE+RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE
Sbjct: 469 LQFLDLIQEGNIGLMKAVDKFEWRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 528

Query: 485 TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544
           TINK+ R SRQ++QE G EP P  IA +M M  EK+RK++KIAKEP+S+E+PVGD+EDSH
Sbjct: 529 TINKLVRTSRQMVQEMGREPTPEEIAERMSMSLEKVRKVLKIAKEPISLETPVGDEEDSH 588

Query: 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGK 604
           LGDFIED++ML+PS+ A+ +++R     +L +LT RE  VLRMRFGI + +DHTLEEVGK
Sbjct: 589 LGDFIEDKSMLSPSEHAIMSNLRDTTGRVLQTLTSREEHVLRMRFGIGLPTDHTLEEVGK 648

Query: 605 QFDVTRERIRQIEAKALRKLR 625
           QF+VTRERIRQIEAKALRKLR
Sbjct: 649 QFNVTRERIRQIEAKALRKLR 669


>gi|377555836|ref|ZP_09785564.1| RNA polymerase, sigma 70 subunit, RpoD [endosymbiont of Bathymodiolus
            sp.]
          Length = 603

 Score =  515 bits (1327), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 290/600 (48%), Positives = 407/600 (67%), Gaps = 18/600 (3%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 894
            +I LGKE+GYLT+SE+ND LP+D++  E IE I      +DI +SE + D +TL++ S  
Sbjct: 15   IIMLGKEKGYLTYSELNDLLPKDLLTQEQIEPIKTILEELDIVISETIPDADTLVVESGA 74

Query: 895  TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 954
             +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL ++ EI IAK IE G+ ++
Sbjct: 75   KAQSTSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKEIEAGVFEI 134

Query: 955  IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNFSSNNRVI-KGNKNNNEEK 1011
            + AI+  P    +   A  ++ + + KI +++ G     ++F+   +    G+ ++ EE 
Sbjct: 135  MQAITLYPVITEKFFKAHKRLEEGKCKITDVIIGYQGDAEDFAEKKKAFDAGDFDDEEEY 194

Query: 1012 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 1071
              +E        E    L++++++K S      DK  KA +K G+  +  +     +S  
Sbjct: 195  EEMEEMEYAGPDEDQVYLRFDTILKCS------DKYLKANKKHGFRDKKTVAERQKLSTS 248

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
            +  +R   K +  + +T+  ++++V + EK I +  +   GM R  F K+F +NE N +W
Sbjct: 249  LSDLRLAPKLVTTMVETICKRVDKVKEQEKSIQKACLY-AGMDRAQFFKLFTDNETNFDW 307

Query: 1132 VDNET---KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 1188
            +   T   KI++     L  +   I   Q+ L + + ++ L + +L+ +N+    G+ +A
Sbjct: 308  LKKVTLDNKIKNK----LAESKNEIYYAQKNLQDYEEEMQLTITELKALNKLYRRGDRRA 363

Query: 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248
            + AK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYAT
Sbjct: 364  KTAKAQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYAT 423

Query: 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 1308
            WWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E  P  +A++ME+PE 
Sbjct: 424  WWIRQAITRSIADQARTIRIPVHMIETINKLNRVKRQLLQKYGREATPEELAVEMELPEY 483

Query: 1309 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 1368
            KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N  +P D     S++    D+L +L+
Sbjct: 484  KIIKILKIAKEPLSMETPVGDDEDSNIGDFIEDGNASSPVDITTKESLKETTGDLLANLS 543

Query: 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLRHPSR +KL  FLE
Sbjct: 544  PREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPSRAHKLSSFLE 603



 Score =  496 bits (1278), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 281/587 (47%), Positives = 397/587 (67%), Gaps = 18/587 (3%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML-SNI 104
           +I LGKE+GYLT+SE+ND LP+D++  E IE I      +DI +SE + D +TL++ S  
Sbjct: 15  IIMLGKEKGYLTYSELNDLLPKDLLTQEQIEPIKTILEELDIVISETIPDADTLVVESGA 74

Query: 105 TSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDM 164
            +     EA  AAL+ +DS+FGRT DP++MYMREMG V+LL ++ EI IAK IE G+ ++
Sbjct: 75  KAQSTSAEAAVAALAALDSEFGRTTDPVRMYMREMGVVDLLEQEDEIRIAKEIEAGVFEI 134

Query: 165 IHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLID--KNFSSNNRVI-KGNKNNNEEK 221
           + AI+  P    +   A  ++ + + KI +++ G     ++F+   +    G+ ++ EE 
Sbjct: 135 MQAITLYPVITEKFFKAHKRLEEGKCKITDVIIGYQGDAEDFAEKKKAFDAGDFDDEEEY 194

Query: 222 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 281
             +E        E    L++++++K S      DK  KA +K G+  +  +     +S  
Sbjct: 195 EEMEEMEYAGPDEDQVYLRFDTILKCS------DKYLKANKKHGFRDKKTVAERQKLSTS 248

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           +  +R   K +  + +T+  ++++V + EK I +  +   GM R  F K+F +NE N +W
Sbjct: 249 LSDLRLAPKLVTTMVETICKRVDKVKEQEKSIQKACLY-AGMDRAQFFKLFTDNETNFDW 307

Query: 342 VDNET---KIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKA 398
           +   T   KI++     L  +   I   Q+ L + + ++ L + +L+ +N+    G+ +A
Sbjct: 308 LKKVTLDNKIKNK----LAESKNEIYYAQKNLQDYEEEMQLTITELKALNKLYRRGDRRA 363

Query: 399 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458
           + AK +M EANLRLVISIAKKY +RGLQFLDLIQEGN+GLMKAVDKFEYRRGYKFSTYAT
Sbjct: 364 KTAKAQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYAT 423

Query: 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518
           WWIRQAITRSIADQARTIRIPVHMIETINK++R+ RQ+LQ+ G E  P  +A++ME+PE 
Sbjct: 424 WWIRQAITRSIADQARTIRIPVHMIETINKLNRVKRQLLQKYGREATPEELAVEMELPEY 483

Query: 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578
           KI KI+KIAKEP+SME+PVGDDEDS++GDFIED N  +P D     S++    D+L +L+
Sbjct: 484 KIIKILKIAKEPLSMETPVGDDEDSNIGDFIEDGNASSPVDITTKESLKETTGDLLANLS 543

Query: 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           PRE+KVL+MRFGI+M++DHTLEEVG+QFDVTRERIRQIEAKALRKLR
Sbjct: 544 PREAKVLKMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLR 590


>gi|329910007|ref|ZP_08275189.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
            IMCC9480]
 gi|327546317|gb|EGF31339.1| RNA polymerase sigma factor RpoD [Oxalobacteraceae bacterium
            IMCC9480]
          Length = 452

 Score =  514 bits (1324), Expect = e-142,   Method: Composition-based stats.
 Identities = 255/418 (61%), Positives = 331/418 (79%)

Query: 1012 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 1071
            +L ++ S  LS  QL  LK  SL +F  I     +M  A   +G++  +Y  A   IS E
Sbjct: 34   VLSQADSDMLSAAQLANLKRTSLARFETIGQQHARMLVAAAADGFHCSAYADAQAIISAE 93

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
            ML +RFTAK ++KL ++LR Q++++  IEKQ+LE+VVN+ GMPR  FI  FP NEI+L W
Sbjct: 94   MLRMRFTAKMVQKLSESLRAQMSEMRGIEKQVLELVVNRGGMPRSLFIATFPGNEIDLGW 153

Query: 1132 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 1191
            +D     Q  Y + L R IP+IKELQ +L+ LQ  + LPL  LR ++++M  GE++AR+A
Sbjct: 154  IDLVVAGQQAYCVTLARQIPAIKELQTRLVALQERVGLPLPQLRRVSKQMSTGELRARQA 213

Query: 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251
            KR+MTEANLRLV+SIAKKY +RG+QFLDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWI
Sbjct: 214  KRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWI 273

Query: 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 1311
            RQA++R+IADQARTIR+PVHM+ET+NK++RI+R+ILQETG E D   +A+ ME+ E+K+R
Sbjct: 274  RQAVSRAIADQARTIRVPVHMLETVNKLNRIARRILQETGVEADLPTLALHMELTEQKVR 333

Query: 1312 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
            +IMKIA+EP+SMESPVGDD DS LGDFI+D    AP +AA++ASMR+ +K++L++L PRE
Sbjct: 334  EIMKIAREPISMESPVGDDGDSQLGDFIQDSTTTAPLEAAVDASMRTAIKEVLDALPPRE 393

Query: 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            +K+LRMR+G++  SDHTLEEVGKQF+VTRERIRQIE+KAL KLRHPSR  KLKIF+EG
Sbjct: 394  AKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQIESKALVKLRHPSRADKLKIFVEG 451



 Score =  493 bits (1269), Expect = e-136,   Method: Composition-based stats.
 Identities = 244/404 (60%), Positives = 319/404 (78%)

Query: 222 ILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNE 281
           +L ++ S  LS  QL  LK  SL +F  I     +M  A   +G++  +Y  A   IS E
Sbjct: 34  VLSQADSDMLSAAQLANLKRTSLARFETIGQQHARMLVAAAADGFHCSAYADAQAIISAE 93

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           ML +RFTAK ++KL ++LR Q++++  IEKQ+LE+VVN+ GMPR  FI  FP NEI+L W
Sbjct: 94  MLRMRFTAKMVQKLSESLRAQMSEMRGIEKQVLELVVNRGGMPRSLFIATFPGNEIDLGW 153

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
           +D     Q  Y + L R IP+IKELQ +L+ LQ  + LPL  LR ++++M  GE++AR+A
Sbjct: 154 IDLVVAGQQAYCVTLARQIPAIKELQTRLVALQERVGLPLPQLRRVSKQMSTGELRARQA 213

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           KR+MTEANLRLV+SIAKKY +RG+QFLDLIQEGNIGL+KAVDKFEYRRGYKFSTYATWWI
Sbjct: 214 KRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWWI 273

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQA++R+IADQARTIR+PVHM+ET+NK++RI+R+ILQETG E D   +A+ ME+ E+K+R
Sbjct: 274 RQAVSRAIADQARTIRVPVHMLETVNKLNRIARRILQETGVEADLPTLALHMELTEQKVR 333

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           +IMKIA+EP+SMESPVGDD DS LGDFI+D    AP +AA++ASMR+ +K++L++L PRE
Sbjct: 334 EIMKIAREPISMESPVGDDGDSQLGDFIQDSTTTAPLEAAVDASMRTAIKEVLDALPPRE 393

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +K+LRMR+G++  SDHTLEEVGKQF+VTRERIRQIE+KAL KLR
Sbjct: 394 AKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQIESKALVKLR 437


>gi|163796954|ref|ZP_02190910.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
 gi|159177701|gb|EDP62252.1| RNA polymerase sigma factor rpoD [alpha proteobacterium BAL199]
          Length = 639

 Score =  512 bits (1319), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 289/622 (46%), Positives = 395/622 (63%), Gaps = 30/622 (4%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            ++N+ +  K LIK GKERG+LT+ E+N  LP++ +  E IE I+     M ++V E+  D
Sbjct: 28   MDNINQAVKNLIKKGKERGFLTYDEVNAALPQEEMSSEQIEDIMSALNEMGVNVVENEDD 87

Query: 886  TETLMLSNITSDDDVE-EATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
                       D   E E TEA L+    D D GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 88   ----------GDQSAEKEDTEAKLAGNVSDDDVGRTDDPVRMYLREMGSVELLSREGEIA 137

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD------GLIDKNFSS 996
            IAKRIE G + MI  I   P T+  ++   D++ +  + + +I+D        ++ N +S
Sbjct: 138  IAKRIEAGREMMIGGICESPLTLRALVNWRDQLKEGTVLLRDIIDLEATYGAEVETNDTS 197

Query: 997  NNRVIKGNKNNNEEKILIESSSADLST--EQLEKLKYESLIKFSNI--------SFHFDK 1046
                 +  +  N++    E ++  LS   +QL     E+  K ++            FDK
Sbjct: 198  TTTEGEETEGENDDDSDDEENNPSLSAMEQQLLPQVLETFDKIADTYGKMVRMQKRRFDK 257

Query: 1047 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 1106
            ++   E        Y K    +   M  +R     IE L + L     +++Q++ ++ + 
Sbjct: 258  LKGGEELARTTERKYEKLKGELIEGMESVRLHNARIEALVEQLYTLNRRLSQVDIRLWK- 316

Query: 1107 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 1166
              ++ G+ R  F++    NE+  +W++    +   +          + E ++ L  +  D
Sbjct: 317  QADRVGVSRKSFMEEHFGNELEPDWLERVATVDARWRKFAETAAEEVSEAREHLAMISAD 376

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              L + + R I + +  GE +A +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 377  AGLTIGEFRRIVQTVQKGEREAGRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 436

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ R SRQ+
Sbjct: 437  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQM 496

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+N + 
Sbjct: 497  LHEIGREPTPEELAEKLVMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQ 556

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P DAA++A++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIRQI
Sbjct: 557  PLDAAIHANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 616

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKL+HPSR  KL+ FL+
Sbjct: 617  EAKALRKLKHPSRSRKLRSFLD 638



 Score =  495 bits (1275), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 281/609 (46%), Positives = 385/609 (63%), Gaps = 30/609 (4%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           ++N+ +  K LIK GKERG+LT+ E+N  LP++ +  E IE I+     M ++V E+  D
Sbjct: 28  MDNINQAVKNLIKKGKERGFLTYDEVNAALPQEEMSSEQIEDIMSALNEMGVNVVENEDD 87

Query: 96  TETLMLSNITSDDDVE-EATEAALS--TVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
                      D   E E TEA L+    D D GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 88  ----------GDQSAEKEDTEAKLAGNVSDDDVGRTDDPVRMYLREMGSVELLSREGEIA 137

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD------GLIDKNFSS 206
           IAKRIE G + MI  I   P T+  ++   D++ +  + + +I+D        ++ N +S
Sbjct: 138 IAKRIEAGREMMIGGICESPLTLRALVNWRDQLKEGTVLLRDIIDLEATYGAEVETNDTS 197

Query: 207 NNRVIKGNKNNNEEKILIESSSADLST--EQLEKLKYESLIKFSNI--------SFHFDK 256
                +  +  N++    E ++  LS   +QL     E+  K ++            FDK
Sbjct: 198 TTTEGEETEGENDDDSDDEENNPSLSAMEQQLLPQVLETFDKIADTYGKMVRMQKRRFDK 257

Query: 257 MRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEI 316
           ++   E        Y K    +   M  +R     IE L + L     +++Q++ ++ + 
Sbjct: 258 LKGGEELARTTERKYEKLKGELIEGMESVRLHNARIEALVEQLYTLNRRLSQVDIRLWK- 316

Query: 317 VVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTD 376
             ++ G+ R  F++    NE+  +W++    +   +          + E ++ L  +  D
Sbjct: 317 QADRVGVSRKSFMEEHFGNELEPDWLERVATVDARWRKFAETAAEEVSEAREHLAMISAD 376

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             L + + R I + +  GE +A +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 377 AGLTIGEFRRIVQTVQKGEREAGRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 436

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ R SRQ+
Sbjct: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQM 496

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+N + 
Sbjct: 497 LHEIGREPTPEELAEKLVMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAVQ 556

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P DAA++A++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIRQI
Sbjct: 557 PLDAAIHANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 616

Query: 617 EAKALRKLR 625
           EAKALRKL+
Sbjct: 617 EAKALRKLK 625


>gi|294669659|ref|ZP_06734726.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
 gi|291308572|gb|EFE49815.1| hypothetical protein NEIELOOT_01560 [Neisseria elongata subsp.
            glycolytica ATCC 29315]
          Length = 496

 Score =  512 bits (1319), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 269/495 (54%), Positives = 356/495 (71%), Gaps = 16/495 (3%)

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN--------- 1004
            MI AIS+CP +I EIL   +KI  +EIK+DE+V+ +ID N    N +  G+         
Sbjct: 1    MIQAISACPGSIAEILELIEKIRNDEIKVDEVVEAIIDPNEVLLNELGLGHLETVPPGAR 60

Query: 1005 -------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 1057
                   ++ + E    E  +AD+ +  LE+LK E L  F+ I   +  M +A       
Sbjct: 61   PGDNAEEESEDGEDEDGEGDAADMGSVNLEELKREVLEHFAVIKDSYGLMVEALNANDSK 120

Query: 1058 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 1117
               Y+K  + I++++L +RF  + IE L ++LR +++ + ++E++I +I +++  M R +
Sbjct: 121  HPEYLKHRDAIAHKLLEVRFATRQIESLSNSLRQKVDNIRKLEREIRDICLDRVQMDRDY 180

Query: 1118 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 1177
            FI  F  N  +L W++NE   +  +   L R   +I E Q +L  ++    + + +L++I
Sbjct: 181  FISQFLPNITDLTWLENEIAKRRVWANALERFQHAILEKQSELAEMEKTAQISIEELKEI 240

Query: 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 1237
            N+ M + E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 241  NKNMQSSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 300

Query: 1238 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 1297
            RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQETG +PD +
Sbjct: 301  RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEDPDSA 360

Query: 1298 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 1357
             +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA+ +S+R
Sbjct: 361  KLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMYSSLR 420

Query: 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417
             V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHP
Sbjct: 421  EVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 480

Query: 1418 SRYYKLKIFLEGKKN 1432
            +R  +LK FL+ + N
Sbjct: 481  TRSDRLKSFLDSEDN 495



 Score =  495 bits (1274), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 261/478 (54%), Positives = 344/478 (71%), Gaps = 16/478 (3%)

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGN--------- 214
           MI AIS+CP +I EIL   +KI  +EIK+DE+V+ +ID N    N +  G+         
Sbjct: 1   MIQAISACPGSIAEILELIEKIRNDEIKVDEVVEAIIDPNEVLLNELGLGHLETVPPGAR 60

Query: 215 -------KNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYN 267
                  ++ + E    E  +AD+ +  LE+LK E L  F+ I   +  M +A       
Sbjct: 61  PGDNAEEESEDGEDEDGEGDAADMGSVNLEELKREVLEHFAVIKDSYGLMVEALNANDSK 120

Query: 268 SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLH 327
              Y+K  + I++++L +RF  + IE L ++LR +++ + ++E++I +I +++  M R +
Sbjct: 121 HPEYLKHRDAIAHKLLEVRFATRQIESLSNSLRQKVDNIRKLEREIRDICLDRVQMDRDY 180

Query: 328 FIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDI 387
           FI  F  N  +L W++NE   +  +   L R   +I E Q +L  ++    + + +L++I
Sbjct: 181 FISQFLPNITDLTWLENEIAKRRVWANALERFQHAILEKQSELAEMEKTAQISIEELKEI 240

Query: 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEY 447
           N+ M + E +  +AK EM +ANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEY
Sbjct: 241 NKNMQSSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 300

Query: 448 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPS 507
           RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK++RISRQ LQETG +PD +
Sbjct: 301 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEDPDSA 360

Query: 508 VIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMR 567
            +A  MEMPE+KIRKIMKIAKEP+SME+P+GDD+DSHLGDFIED N +AP+DAA+ +S+R
Sbjct: 361 KLAELMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMYSSLR 420

Query: 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            V  D+L SLTPRE+KVLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 421 EVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 478


>gi|167648221|ref|YP_001685884.1| RNA polymerase sigma factor RpoD [Caulobacter sp. K31]
 gi|167350651|gb|ABZ73386.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter sp. K31]
          Length = 649

 Score =  512 bits (1318), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 287/628 (45%), Positives = 399/628 (63%), Gaps = 39/628 (6%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            KKF   IK  K RGY+T  E+N  LP + +  E IE  +     M ++V E   D ET  
Sbjct: 30   KKF---IKQAKARGYVTMDELNKVLPSEEVTSEAIEDTLAMLSEMGVNVVEAEEDAETSE 86

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
               + + +D ++      S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87   GGEVVAREDNQQVI---TSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI--------- 1001
               MI  +     T   I++  +++    I + E++D  ++  +++ N V          
Sbjct: 144  RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYAAINGVAAAPAADDEP 201

Query: 1002 ---KGNKNNNEEKILIESSSADL------STEQLE-KLKYESLIKFSNISFHFDKMRKAF 1051
                  +  +E K   E    D       +   +E +L+   +     I+  F+  RK  
Sbjct: 202  AEPSDEEPGSEPKAEGEEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFETFRKLQ 261

Query: 1052 EK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVTQIE 1100
            +K      +G + S++  KA+  +SN ++     ++     IE L + L     ++  +E
Sbjct: 262  DKLVGSRLKGADLSDADRKAYEGLSNTIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLE 321

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 1160
             ++L +  +  G+ R  F+K +  +E+N NW+D    +   +   +  +  S+ +++Q++
Sbjct: 322  GRLLRLA-DSYGISRSEFLKAYFGSELNPNWIDQVKAMGVRWTKFVENDTNSVGDIRQEI 380

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
              L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 381  AALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDL 440

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 
Sbjct: 441  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIV 500

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 501  RTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 560

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTR
Sbjct: 561  DKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTR 620

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 621  ERIRQIEAKALRKLKHPSRSRKLRSFLD 648



 Score =  494 bits (1273), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 279/615 (45%), Positives = 389/615 (63%), Gaps = 39/615 (6%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           KKF   IK  K RGY+T  E+N  LP + +  E IE  +     M ++V E   D ET  
Sbjct: 30  KKF---IKQAKARGYVTMDELNKVLPSEEVTSEAIEDTLAMLSEMGVNVVEAEEDAETSE 86

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
              + + +D ++      S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87  GGEVVAREDNQQVI---TSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI--------- 211
              MI  +     T   I++  +++    I + E++D  ++  +++ N V          
Sbjct: 144 RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYAAINGVAAAPAADDEP 201

Query: 212 ---KGNKNNNEEKILIESSSADL------STEQLE-KLKYESLIKFSNISFHFDKMRKAF 261
                 +  +E K   E    D       +   +E +L+   +     I+  F+  RK  
Sbjct: 202 AEPSDEEPGSEPKAEGEEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFETFRKLQ 261

Query: 262 EK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVTQIE 310
           +K      +G + S++  KA+  +SN ++     ++     IE L + L     ++  +E
Sbjct: 262 DKLVGSRLKGADLSDADRKAYEGLSNTIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLE 321

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKL 370
            ++L +  +  G+ R  F+K +  +E+N NW+D    +   +   +  +  S+ +++Q++
Sbjct: 322 GRLLRLA-DSYGISRSEFLKAYFGSELNPNWIDQVKAMGVRWTKFVENDTNSVGDIRQEI 380

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
             L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 381 AALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDL 440

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 
Sbjct: 441 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIV 500

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 501 RTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 560

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTR
Sbjct: 561 DKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTR 620

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKL+
Sbjct: 621 ERIRQIEAKALRKLK 635


>gi|399069393|ref|ZP_10749391.1| RNA polymerase sigma factor, sigma-70 family [Caulobacter sp. AP07]
 gi|398045171|gb|EJL37927.1| RNA polymerase sigma factor, sigma-70 family [Caulobacter sp. AP07]
          Length = 650

 Score =  511 bits (1317), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 284/630 (45%), Positives = 399/630 (63%), Gaps = 42/630 (6%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            KKF   IK  K RGY+T  E+N  LP + +  E IE  +     M ++V E   D ET  
Sbjct: 30   KKF---IKQAKARGYVTMDELNKVLPSEEVTSEAIEDTLAMLSEMGVNVVEAEEDAETSE 86

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
               + + +D ++      S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87   GGEVVAREDNQQVI---TSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI--------- 1001
               MI  +     T   I++  +++    I + E++D  ++  +++ N V          
Sbjct: 144  RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYTAINGVAAAIAAEEAE 201

Query: 1002 ------------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 1049
                        K     ++E    + +   +S  + E L+   +     I+  F+  RK
Sbjct: 202  QAEPVEADPDAPKAEGEGDDEDDFDDGAGPTVSAMEGE-LREGVMAILDAIASEFETFRK 260

Query: 1050 AFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVTQ 1098
              +K      +G + S++  KA+  +S  ++     ++     IE L + L     ++  
Sbjct: 261  LQDKLVGSRLKGADLSDADRKAYEGLSQTIIQHLKTLKLNNARIEALVEQLYAINKRLIG 320

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 1158
            +E ++L +  +  G+ R  F+K +  +E+N NW++    +   +   +  ++ S+ +++Q
Sbjct: 321  LEGRLLRLA-DSYGISRSEFLKAYFGSELNPNWIEQVKAMGVRWTKFVENDVNSVGDIRQ 379

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            ++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 380  EIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 439

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 440  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 499

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            I R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 500  IVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 559

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF V
Sbjct: 560  IEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 619

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 620  TRERIRQIEAKALRKLKHPSRSRKLRSFLD 649



 Score =  494 bits (1272), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 276/617 (44%), Positives = 389/617 (63%), Gaps = 42/617 (6%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           KKF   IK  K RGY+T  E+N  LP + +  E IE  +     M ++V E   D ET  
Sbjct: 30  KKF---IKQAKARGYVTMDELNKVLPSEEVTSEAIEDTLAMLSEMGVNVVEAEEDAETSE 86

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
              + + +D ++      S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87  GGEVVAREDNQQVI---TSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI--------- 211
              MI  +     T   I++  +++    I + E++D  ++  +++ N V          
Sbjct: 144 RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYTAINGVAAAIAAEEAE 201

Query: 212 ------------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRK 259
                       K     ++E    + +   +S  + E L+   +     I+  F+  RK
Sbjct: 202 QAEPVEADPDAPKAEGEGDDEDDFDDGAGPTVSAMEGE-LREGVMAILDAIASEFETFRK 260

Query: 260 AFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVTQ 308
             +K      +G + S++  KA+  +S  ++     ++     IE L + L     ++  
Sbjct: 261 LQDKLVGSRLKGADLSDADRKAYEGLSQTIIQHLKTLKLNNARIEALVEQLYAINKRLIG 320

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQ 368
           +E ++L +  +  G+ R  F+K +  +E+N NW++    +   +   +  ++ S+ +++Q
Sbjct: 321 LEGRLLRLA-DSYGISRSEFLKAYFGSELNPNWIEQVKAMGVRWTKFVENDVNSVGDIRQ 379

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           ++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 380 EIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFL 439

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 440 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 499

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           I R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 500 IVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 559

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF V
Sbjct: 560 IEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSV 619

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKL+
Sbjct: 620 TRERIRQIEAKALRKLK 636


>gi|347758338|ref|YP_004865900.1| RNA polymerase sigma factor RpoD [Micavibrio aeruginosavorus ARL-13]
 gi|347590856|gb|AEP09898.1| RNA polymerase sigma factor RpoD [Micavibrio aeruginosavorus ARL-13]
          Length = 831

 Score =  510 bits (1313), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 289/646 (44%), Positives = 405/646 (62%), Gaps = 50/646 (7%)

Query: 810  KKNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESII 869
            ++ A + D  +  R  +E++ KK   L+  GKERG+LT+ EIN  +P +    E IE  +
Sbjct: 208  QQEAATDDAPAKPRGSLESIVKK---LVTKGKERGFLTYDEINSAIPAEEFSSEQIEDAM 264

Query: 870  KTFRYMDISVSEHVLDTETLMLSNITSDDDVEEA-------TEAALSTVDSDFGRTKDPI 922
             T   + I +              + S+DDVEEA       +   +S+ DS  GRT DP+
Sbjct: 265  ATMSDVGIQL--------------VDSEDDVEEAEKGEEYESSGNISSDDS--GRTDDPV 308

Query: 923  KMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKI 982
            +MY+REMGSVELL+R+GEI IAKRIE G + MI  I   P  I  ++   + + K +I +
Sbjct: 309  RMYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLAIESMIAWYEALQKGDILL 368

Query: 983  DEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIES--------SSADLSTEQLEKLKYESL 1034
             E++D  +D  +  ++       + +E +             ++  LS  + E L   S 
Sbjct: 369  REVID--LDATYGDSSDGAPPADDLDEPEGESAEGAEGGEEENAVSLSAMEQELLPQVSE 426

Query: 1035 IKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIE 1083
              FS I   + KM+K           A +     ++ Y      +   M  +R     IE
Sbjct: 427  -SFSKIQKTYKKMQKVQQERFEHLQNAKQPPAATNKKYDDLKAQMVELMNEVRLNNARIE 485

Query: 1084 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDY 1142
            +L   L     +V  +E +++ + V+ CG+ R  F++ +  +E++ NW+    K+    +
Sbjct: 486  QLVGRLYKMNREVVSLEGRLMRLAVD-CGVKREDFLQNYYGSELDPNWLAKVAKLTGKGW 544

Query: 1143 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 1202
                 +++  + E++ +++ +  D  +PL + R I   +  GE +A +AK+EM EANLRL
Sbjct: 545  AKFAEKHVAEVGEIRTQIVTVTDDAGVPLGEFRRIVGTVQKGEREAARAKKEMVEANLRL 604

Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
            VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 605  VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 664

Query: 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 1322
            ARTIRIPVHMIETINK+ R SRQ++ E G EP P  +A ++ MP +K+RK++KIAKEPVS
Sbjct: 665  ARTIRIPVHMIETINKLVRTSRQMMHEIGREPTPEELAERLHMPLDKVRKVLKIAKEPVS 724

Query: 1323 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 1382
            +E+P+GD+EDS LGDFIED+N L P DAA+++++R     +L +LTPRE +VLRMRFGI 
Sbjct: 725  LETPIGDEEDSTLGDFIEDKNALLPVDAAIHSNLRETTTRVLATLTPREERVLRMRFGIG 784

Query: 1383 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 785  MNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 830



 Score =  492 bits (1266), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 281/632 (44%), Positives = 394/632 (62%), Gaps = 50/632 (7%)

Query: 21  KNAFSFDIKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIK 80
           + A + D  +  R  +E++ KK   L+  GKERG+LT+ EIN  +P +    E IE  + 
Sbjct: 209 QEAATDDAPAKPRGSLESIVKK---LVTKGKERGFLTYDEINSAIPAEEFSSEQIEDAMA 265

Query: 81  TFRYMDISVSEHVLDTETLMLSNITSDDDVEEA-------TEAALSTVDSDFGRTKDPIK 133
           T   + I +              + S+DDVEEA       +   +S+ DS  GRT DP++
Sbjct: 266 TMSDVGIQL--------------VDSEDDVEEAEKGEEYESSGNISSDDS--GRTDDPVR 309

Query: 134 MYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKID 193
           MY+REMGSVELL+R+GEI IAKRIE G + MI  I   P  I  ++   + + K +I + 
Sbjct: 310 MYLREMGSVELLSREGEIAIAKRIEAGREMMIGGICESPLAIESMIAWYEALQKGDILLR 369

Query: 194 EIVDGLIDKNFSSNNRVIKGNKNNNEEKILIES--------SSADLSTEQLEKLKYESLI 245
           E++D  +D  +  ++       + +E +             ++  LS  + E L   S  
Sbjct: 370 EVID--LDATYGDSSDGAPPADDLDEPEGESAEGAEGGEEENAVSLSAMEQELLPQVSE- 426

Query: 246 KFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEK 294
            FS I   + KM+K           A +     ++ Y      +   M  +R     IE+
Sbjct: 427 SFSKIQKTYKKMQKVQQERFEHLQNAKQPPAATNKKYDDLKAQMVELMNEVRLNNARIEQ 486

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYN 353
           L   L     +V  +E +++ + V+ CG+ R  F++ +  +E++ NW+    K+    + 
Sbjct: 487 LVGRLYKMNREVVSLEGRLMRLAVD-CGVKREDFLQNYYGSELDPNWLAKVAKLTGKGWA 545

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +++  + E++ +++ +  D  +PL + R I   +  GE +A +AK+EM EANLRLV
Sbjct: 546 KFAEKHVAEVGEIRTQIVTVTDDAGVPLGEFRRIVGTVQKGEREAARAKKEMVEANLRLV 605

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 606 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 665

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINK+ R SRQ++ E G EP P  +A ++ MP +K+RK++KIAKEPVS+
Sbjct: 666 RTIRIPVHMIETINKLVRTSRQMMHEIGREPTPEELAERLHMPLDKVRKVLKIAKEPVSL 725

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GD+EDS LGDFIED+N L P DAA+++++R     +L +LTPRE +VLRMRFGI M
Sbjct: 726 ETPIGDEEDSTLGDFIEDKNALLPVDAAIHSNLRETTTRVLATLTPREERVLRMRFGIGM 785

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 786 NTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 817


>gi|349685585|ref|ZP_08896727.1| RNA polymerase sigma factor RpoD [Gluconacetobacter oboediens 174Bp2]
          Length = 669

 Score =  509 bits (1311), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 294/638 (46%), Positives = 392/638 (61%), Gaps = 44/638 (6%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 891
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    +TET   
Sbjct: 31   KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDETETPAA 90

Query: 892  SNITSDDDVEEATEA-------------ALSTVDSD-FGRTKDPIKMYMREMGSVELLTR 937
            +   SDD  EE TE+             A   VD++  GRT DP++MY+REMGSVELL+R
Sbjct: 91   TETKSDDTAEEETESDDTAEEETESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSR 150

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------- 987
            +GEI IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD          
Sbjct: 151  EGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGGND 210

Query: 988  ----GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISF 1042
                   D+ F  +           E +   E   A LS   LE KLK E L +F  +  
Sbjct: 211  PAEAAEGDEAFGESEGAENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEA 270

Query: 1043 HFDKMRK--AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRN 1091
             +  + K  A   E + + + I   +    E L +    K          IE L + L+ 
Sbjct: 271  LYAALHKVQAERLEKFTAGAEISVDDESRYERLRMELVGKVQQVHLHNARIEVLVEHLKE 330

Query: 1092 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNI 1150
               ++  +E ++L +      + R  F+  +   E++  W+D   T     +   L ++ 
Sbjct: 331  IFQRLNGLEGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMVATLPAKSWKNFLAKHG 389

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
             ++  L+ ++ +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKY
Sbjct: 390  ETVIRLRNQVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKY 449

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 450  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 509

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+
Sbjct: 510  HMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDE 569

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            EDSHLGDFIED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLE
Sbjct: 570  EDSHLGDFIEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLE 629

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 630  EVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 667



 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 286/625 (45%), Positives = 382/625 (61%), Gaps = 44/625 (7%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 101
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    +TET   
Sbjct: 31  KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDETETPAA 90

Query: 102 SNITSDDDVEEATEA-------------ALSTVDSD-FGRTKDPIKMYMREMGSVELLTR 147
           +   SDD  EE TE+             A   VD++  GRT DP++MY+REMGSVELL+R
Sbjct: 91  TETKSDDTAEEETESDDTAEEETESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSR 150

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------- 197
           +GEI IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD          
Sbjct: 151 EGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGGND 210

Query: 198 ----GLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISF 252
                  D+ F  +           E +   E   A LS   LE KLK E L +F  +  
Sbjct: 211 PAEAAEGDEAFGESEGAENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEA 270

Query: 253 HFDKMRK--AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRN 301
            +  + K  A   E + + + I   +    E L +    K          IE L + L+ 
Sbjct: 271 LYAALHKVQAERLEKFTAGAEISVDDESRYERLRMELVGKVQQVHLHNARIEVLVEHLKE 330

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNI 360
              ++  +E ++L +      + R  F+  +   E++  W+D   T     +   L ++ 
Sbjct: 331 IFQRLNGLEGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMVATLPAKSWKNFLAKHG 389

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
            ++  L+ ++ +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKY
Sbjct: 390 ETVIRLRNQVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKY 449

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 450 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 509

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+
Sbjct: 510 HMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDE 569

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           EDSHLGDFIED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLE
Sbjct: 570 EDSHLGDFIEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLE 629

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 630 EVGQQFNVTRERIRQIEAKALRKLK 654


>gi|262189558|ref|ZP_06047968.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
 gi|262034560|gb|EEY52890.1| RNA polymerase sigma factor RpoD [Vibrio cholerae CT 5369-93]
          Length = 522

 Score =  509 bits (1310), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 272/528 (51%), Positives = 352/528 (66%), Gaps = 32/528 (6%)

Query: 926  MREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEI 985
            MREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  IL   D++   E+++ ++
Sbjct: 1    MREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDL 60

Query: 986  VDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---------- 1035
            + G +D N          +       I  E S ADL+ E    ++ E             
Sbjct: 61   ISGFVDPNDMETEAPTATH-------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESS 113

Query: 1036 ---------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
                           KF+ +   F  ++ A  + G +S    +A + + +     R T K
Sbjct: 114  DSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPK 173

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 1140
              + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE N  W+D       
Sbjct: 174  QFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDK 233

Query: 1141 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 1200
             Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANL
Sbjct: 234  PYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 293

Query: 1201 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 1260
            RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 294  RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 353

Query: 1261 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 1320
            DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP
Sbjct: 354  DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 413

Query: 1321 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 1380
            +SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFG
Sbjct: 414  ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 473

Query: 1381 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 474  IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 521



 Score =  494 bits (1273), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 265/515 (51%), Positives = 343/515 (66%), Gaps = 32/515 (6%)

Query: 136 MREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEI 195
           MREMG+VELLTR+GEI+IAKRIE+G+  +  AI+  P TI  IL   D++   E+++ ++
Sbjct: 1   MREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDL 60

Query: 196 VDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLI---------- 245
           + G +D N          +       I  E S ADL+ E    ++ E             
Sbjct: 61  ISGFVDPNDMETEAPTATH-------IGSELSEADLADEDDAVVEDEDEDEDEDGDGESS 113

Query: 246 ---------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
                          KF+ +   F  ++ A  + G +S    +A + + +     R T K
Sbjct: 114 DSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPK 173

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQH 350
             + L +TLR  +++V   E+ +++ VV    MP+  FI +F  NE N  W+D       
Sbjct: 174 QFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDK 233

Query: 351 DYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANL 410
            Y   +      I+   QKL  ++ +  L +  ++DI+R+M  GE KAR+AK+EM EANL
Sbjct: 234 PYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANL 293

Query: 411 RLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470
           RLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA
Sbjct: 294 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 353

Query: 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEP 530
           DQARTIRIPVHMIETINK++RISRQ+LQE G EP P  +A +M+MPE+KIRK++KIAKEP
Sbjct: 354 DQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEP 413

Query: 531 VSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFG 590
           +SME+P+GDDEDSHLGDFIED  +  P D+A   S+++  +D+L  LTPRE+KVLRMRFG
Sbjct: 414 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFG 473

Query: 591 IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           I+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 474 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 508


>gi|406989588|gb|EKE09357.1| hypothetical protein ACD_16C00190G0005 [uncultured bacterium]
          Length = 644

 Score =  508 bits (1309), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 289/636 (45%), Positives = 402/636 (63%), Gaps = 57/636 (8%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            K  K L+  GK+RGY+T+ E+N+ LPED +  E IE I+     M I             
Sbjct: 27   KAVKQLLAQGKQRGYITYEELNETLPEDKLSSEQIEDIMSMISDMGI------------- 73

Query: 891  LSNITSDDDVEEATEAALSTVDSD---------FGRTKDPIKMYMREMGSVELLTRDGEI 941
              NI  D++ E+  +   +  D++          G+T DP+++Y+REMGSVELL+R+GEI
Sbjct: 74   --NIVEDEEAEQEDKTKQTAKDNEEEETVEASEVGKTDDPVRLYLREMGSVELLSREGEI 131

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 1001
            EIAKRIE G + MI AI   P TI  I+   D ++K+++ + +I+D  I+  ++ N    
Sbjct: 132  EIAKRIESGREMMIGAICESPLTIRAIVTWRDALNKDQMLLRDIID--IESTYT-NGPSE 188

Query: 1002 KGNKNNNEEKILIESSS----------------ADLSTEQLE-KLKYESLIKFSNISFHF 1044
            +   N +EE  L+ ++                 A LS   +E  L+ + +  F+ I+  +
Sbjct: 189  EDADNFDEEDDLLGNTPLAEEEIEEESEYDDESAGLSVSAMEDSLRPKVVETFNQIAKTY 248

Query: 1045 DKMRK-------AFEKEGYNSESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQI 1093
             ++RK       + +K    S S  K +  I  E++    GI   +  IE+L + L    
Sbjct: 249  TQLRKLQEQRLKSLQKGAKASASTEKKYEEIRKELIELMEGIHLNSSRIEQLVEQLYTLN 308

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPS 1152
             ++  +E ++L +     G+ R  F++ +  +E+   W D  ET     +   L ++   
Sbjct: 309  RKLVGLEGRLLRLA-EAAGVKREVFLENYYGSELAPEWFDKLETLSSKGWKTFLDKHKEE 367

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
               +++ +  +  +  LP+++ R I   +  GE  + +AK+EM EANLRLVISIAKKYT+
Sbjct: 368  ALTIRKIIAEVADESGLPISEFRRILGTVQKGERDSTRAKKEMIEANLRLVISIAKKYTN 427

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 428  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 487

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINK+ R SRQ+L E G EP P  +A K++MP +K+RK+MKIAKEP+S+E+P+GD+ED
Sbjct: 488  IETINKLVRTSRQMLHEIGREPTPEELANKLKMPLDKVRKVMKIAKEPISLETPIGDEED 547

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
             HLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEV
Sbjct: 548  GHLGDFIEDKNAVVPVDAAVLSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 607

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            G+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 608  GQQFAVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 643



 Score =  491 bits (1265), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 281/623 (45%), Positives = 392/623 (62%), Gaps = 57/623 (9%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           K  K L+  GK+RGY+T+ E+N+ LPED +  E IE I+     M I             
Sbjct: 27  KAVKQLLAQGKQRGYITYEELNETLPEDKLSSEQIEDIMSMISDMGI------------- 73

Query: 101 LSNITSDDDVEEATEAALSTVDSD---------FGRTKDPIKMYMREMGSVELLTRDGEI 151
             NI  D++ E+  +   +  D++          G+T DP+++Y+REMGSVELL+R+GEI
Sbjct: 74  --NIVEDEEAEQEDKTKQTAKDNEEEETVEASEVGKTDDPVRLYLREMGSVELLSREGEI 131

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVI 211
           EIAKRIE G + MI AI   P TI  I+   D ++K+++ + +I+D  I+  ++ N    
Sbjct: 132 EIAKRIESGREMMIGAICESPLTIRAIVTWRDALNKDQMLLRDIID--IESTYT-NGPSE 188

Query: 212 KGNKNNNEEKILIESSS----------------ADLSTEQLE-KLKYESLIKFSNISFHF 254
           +   N +EE  L+ ++                 A LS   +E  L+ + +  F+ I+  +
Sbjct: 189 EDADNFDEEDDLLGNTPLAEEEIEEESEYDDESAGLSVSAMEDSLRPKVVETFNQIAKTY 248

Query: 255 DKMRK-------AFEKEGYNSESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQI 303
            ++RK       + +K    S S  K +  I  E++    GI   +  IE+L + L    
Sbjct: 249 TQLRKLQEQRLKSLQKGAKASASTEKKYEEIRKELIELMEGIHLNSSRIEQLVEQLYTLN 308

Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPS 362
            ++  +E ++L +     G+ R  F++ +  +E+   W D  ET     +   L ++   
Sbjct: 309 RKLVGLEGRLLRLA-EAAGVKREVFLENYYGSELAPEWFDKLETLSSKGWKTFLDKHKEE 367

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
              +++ +  +  +  LP+++ R I   +  GE  + +AK+EM EANLRLVISIAKKYT+
Sbjct: 368 ALTIRKIIAEVADESGLPISEFRRILGTVQKGERDSTRAKKEMIEANLRLVISIAKKYTN 427

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 428 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 487

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINK+ R SRQ+L E G EP P  +A K++MP +K+RK+MKIAKEP+S+E+P+GD+ED
Sbjct: 488 IETINKLVRTSRQMLHEIGREPTPEELANKLKMPLDKVRKVMKIAKEPISLETPIGDEED 547

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
            HLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEV
Sbjct: 548 GHLGDFIEDKNAVVPVDAAVLSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 607

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           G+QF VTRERIRQIEAKALRKL+
Sbjct: 608 GQQFAVTRERIRQIEAKALRKLK 630


>gi|407781744|ref|ZP_11128961.1| RNA polymerase sigma factor RpoD [Oceanibaculum indicum P24]
 gi|407207370|gb|EKE77307.1| RNA polymerase sigma factor RpoD [Oceanibaculum indicum P24]
          Length = 652

 Score =  508 bits (1309), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 292/635 (45%), Positives = 397/635 (62%), Gaps = 39/635 (6%)

Query: 826  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 885
            I+N+    K LI+ GKERGY+T+ E+N  LP D +  E IE I+     M ++V +    
Sbjct: 24   IDNIGAAVKRLIQKGKERGYITYDELNAALPSDQMSSEQIEDIMTQLSEMGVNVIDDEDK 83

Query: 886  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
             E        + DD E+  +   +  D D GRT DP++MY+REMGSVELL+R+GEI IAK
Sbjct: 84   EEREDRG--AAGDDDEDVVKGG-NIDDDDIGRTDDPVRMYLREMGSVELLSREGEIAIAK 140

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 1005
            RIE G + MI  I   P T   IL   D +    I + +I+D  +D  + +     +   
Sbjct: 141  RIEAGREAMIGGICESPLTFDAILAWRDALLDGRILLRDIID--LDATYGAGPDAEEAEG 198

Query: 1006 NNNEEKILIES---------------------SSADLSTEQLEKLKYESLIKFSNISFHF 1044
            +   ++    +                     ++  LS  + E LK   L +   I+  +
Sbjct: 199  DGEGDEEAAPAEAKENQPEGESEEAEEGDEDDNTMSLSAMEAE-LKPMVLEQLDQIAESY 257

Query: 1045 DKMRKAFEK--------EGYNSES---YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
             K++K  E+        E    +S   Y +  + +   M  IR     IE L + +    
Sbjct: 258  GKLQKLQERRLLKIQKGEALTKQSEAKYEQQRSELVEMMNKIRLNNSRIEALMEQIYELN 317

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 1153
             ++T +E +IL +     G+ R  F+K +  NE++ NW++        ++  L      +
Sbjct: 318  RRLTGLEGRILRLA-ETAGVKRPDFLKAYFGNELDPNWLETLAGRSKAWDKFLTTQEEEV 376

Query: 1154 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 1213
            ++L+Q + ++ ++  LP+ + R I + +  GE +A +AK+EM EANLRLVISIAKKYT+R
Sbjct: 377  RKLRQLVADISSEAALPIGEFRRIVQTVQKGEREASRAKKEMVEANLRLVISIAKKYTNR 436

Query: 1214 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273
            GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 437  GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 496

Query: 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333
            ETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDS
Sbjct: 497  ETINKLVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDS 556

Query: 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 1393
            HLGDFIED+N + P DAA+ A++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG
Sbjct: 557  HLGDFIEDKNAILPVDAAIQANLRETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVG 616

Query: 1394 KQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            +QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 617  QQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 651



 Score =  491 bits (1264), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 284/622 (45%), Positives = 387/622 (62%), Gaps = 39/622 (6%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLD 95
           I+N+    K LI+ GKERGY+T+ E+N  LP D +  E IE I+     M ++V +    
Sbjct: 24  IDNIGAAVKRLIQKGKERGYITYDELNAALPSDQMSSEQIEDIMTQLSEMGVNVIDDEDK 83

Query: 96  TETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
            E        + DD E+  +   +  D D GRT DP++MY+REMGSVELL+R+GEI IAK
Sbjct: 84  EEREDRG--AAGDDDEDVVKGG-NIDDDDIGRTDDPVRMYLREMGSVELLSREGEIAIAK 140

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNK 215
           RIE G + MI  I   P T   IL   D +    I + +I+D  +D  + +     +   
Sbjct: 141 RIEAGREAMIGGICESPLTFDAILAWRDALLDGRILLRDIID--LDATYGAGPDAEEAEG 198

Query: 216 NNNEEKILIES---------------------SSADLSTEQLEKLKYESLIKFSNISFHF 254
           +   ++    +                     ++  LS  + E LK   L +   I+  +
Sbjct: 199 DGEGDEEAAPAEAKENQPEGESEEAEEGDEDDNTMSLSAMEAE-LKPMVLEQLDQIAESY 257

Query: 255 DKMRKAFEK--------EGYNSES---YIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 303
            K++K  E+        E    +S   Y +  + +   M  IR     IE L + +    
Sbjct: 258 GKLQKLQERRLLKIQKGEALTKQSEAKYEQQRSELVEMMNKIRLNNSRIEALMEQIYELN 317

Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSI 363
            ++T +E +IL +     G+ R  F+K +  NE++ NW++        ++  L      +
Sbjct: 318 RRLTGLEGRILRLA-ETAGVKRPDFLKAYFGNELDPNWLETLAGRSKAWDKFLTTQEEEV 376

Query: 364 KELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR 423
           ++L+Q + ++ ++  LP+ + R I + +  GE +A +AK+EM EANLRLVISIAKKYT+R
Sbjct: 377 RKLRQLVADISSEAALPIGEFRRIVQTVQKGEREASRAKKEMVEANLRLVISIAKKYTNR 436

Query: 424 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483
           GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI
Sbjct: 437 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 496

Query: 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543
           ETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDS
Sbjct: 497 ETINKLVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDS 556

Query: 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVG 603
           HLGDFIED+N + P DAA+ A++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG
Sbjct: 557 HLGDFIEDKNAILPVDAAIQANLRETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVG 616

Query: 604 KQFDVTRERIRQIEAKALRKLR 625
           +QF VTRERIRQIEAKALRKL+
Sbjct: 617 QQFSVTRERIRQIEAKALRKLK 638


>gi|209545152|ref|YP_002277381.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
            PAl 5]
 gi|209532829|gb|ACI52766.1| RNA polymerase, sigma 70 subunit, RpoD [Gluconacetobacter
            diazotrophicus PAl 5]
          Length = 650

 Score =  508 bits (1307), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 289/629 (45%), Positives = 391/629 (62%), Gaps = 45/629 (7%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M I V E+          N
Sbjct: 31   KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVVENE--------DN 82

Query: 894  ITSDDDVEEATEAA----------LSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIE 942
              S+ + EE  E A             VD++  GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 83   DDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIA 142

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S       
Sbjct: 143  IAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGAEAEA 200

Query: 1003 GNKNNNEEKILI----------ESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK-- 1049
            G +   +E              E  SA LS   LE KLK E L +F  I   + +++K  
Sbjct: 201  GAEGGEQEDGSFDAAPESEDGEEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 260

Query: 1050 ---------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
                       E    + +SY K    +  ++  +      IE L   L+    ++  +E
Sbjct: 261  SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 320

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQK 1159
             ++L +      + R  F+  +  +E++  W+D  + +    +   + ++  S+ +L+ +
Sbjct: 321  GRMLRLA-ESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQ 379

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            + +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 380  VASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLD 439

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 440  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 499

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
             R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFI
Sbjct: 500  VRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFI 559

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VT
Sbjct: 560  EDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVT 619

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 620  RERIRQIEAKALRKLKHPSRSRKLRSFLD 648



 Score =  490 bits (1262), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 281/616 (45%), Positives = 381/616 (61%), Gaps = 45/616 (7%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M I V E+          N
Sbjct: 31  KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVVENE--------DN 82

Query: 104 ITSDDDVEEATEAA----------LSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIE 152
             S+ + EE  E A             VD++  GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 83  DDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIA 142

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S       
Sbjct: 143 IAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGAEAEA 200

Query: 213 GNKNNNEEKILI----------ESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK-- 259
           G +   +E              E  SA LS   LE KLK E L +F  I   + +++K  
Sbjct: 201 GAEGGEQEDGSFDAAPESEDGEEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 260

Query: 260 ---------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
                      E    + +SY K    +  ++  +      IE L   L+    ++  +E
Sbjct: 261 SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 320

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQK 369
            ++L +      + R  F+  +  +E++  W+D  + +    +   + ++  S+ +L+ +
Sbjct: 321 GRMLRLA-ESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQ 379

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           + +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 380 VASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLD 439

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 440 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 499

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
            R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFI
Sbjct: 500 VRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFI 559

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VT
Sbjct: 560 EDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVT 619

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKL+
Sbjct: 620 RERIRQIEAKALRKLK 635


>gi|162149105|ref|YP_001603566.1| RNA polymerase sigma factor RpoD [Gluconacetobacter diazotrophicus
            PAl 5]
 gi|161787682|emb|CAP57278.1| RNA polymerase sigma factor rpoD (Sigma-A) [Gluconacetobacter
            diazotrophicus PAl 5]
          Length = 656

 Score =  508 bits (1307), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 289/629 (45%), Positives = 391/629 (62%), Gaps = 45/629 (7%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M I V E+          N
Sbjct: 37   KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVVENE--------DN 88

Query: 894  ITSDDDVEEATEAA----------LSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIE 942
              S+ + EE  E A             VD++  GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 89   DDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIA 148

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 1002
            IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S       
Sbjct: 149  IAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGAEAEA 206

Query: 1003 GNKNNNEEKILI----------ESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK-- 1049
            G +   +E              E  SA LS   LE KLK E L +F  I   + +++K  
Sbjct: 207  GAEGGEQEDGSFDAAPESEDGEEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 266

Query: 1050 ---------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 1100
                       E    + +SY K    +  ++  +      IE L   L+    ++  +E
Sbjct: 267  SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 326

Query: 1101 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQK 1159
             ++L +      + R  F+  +  +E++  W+D  + +    +   + ++  S+ +L+ +
Sbjct: 327  GRMLRLA-ESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQ 385

Query: 1160 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 1219
            + +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 386  VASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLD 445

Query: 1220 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 1279
            LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 446  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 505

Query: 1280 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339
             R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFI
Sbjct: 506  VRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFI 565

Query: 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 1399
            ED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VT
Sbjct: 566  EDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVT 625

Query: 1400 RERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 626  RERIRQIEAKALRKLKHPSRSRKLRSFLD 654



 Score =  490 bits (1261), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 281/616 (45%), Positives = 381/616 (61%), Gaps = 45/616 (7%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M I V E+          N
Sbjct: 37  KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAVLSEMGIQVVENE--------DN 88

Query: 104 ITSDDDVEEATEAA----------LSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIE 152
             S+ + EE  E A             VD++  GRT DP++MY+REMGSVELL+R+GEI 
Sbjct: 89  DDSEANREEKAEEADTEGEEAGGAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIA 148

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIK 212
           IAKRIE G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S       
Sbjct: 149 IAKRIEAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGAEAEA 206

Query: 213 GNKNNNEEKILI----------ESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK-- 259
           G +   +E              E  SA LS   LE KLK E L +F  I   + +++K  
Sbjct: 207 GAEGGEQEDGSFDAAPESEDGEEGDSAGLSLSALEEKLKPEILAQFEEIEELYSRLQKLQ 266

Query: 260 ---------AFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIE 310
                      E    + +SY K    +  ++  +      IE L   L+    ++  +E
Sbjct: 267 SKRLETLTSGAEMSDKSEKSYEKLREELVGKVQQVHLHNTRIEVLVQHLKEIFQRLNGLE 326

Query: 311 KQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQK 369
            ++L +      + R  F+  +  +E++  W+D  + +    +   + ++  S+ +L+ +
Sbjct: 327 GRMLRLA-ESTKVSREDFLIKYRGSELDPGWMDMVSALPGKAWKNFVAKHSASVLDLRGQ 385

Query: 370 LINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLD 429
           + +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLD
Sbjct: 386 VASLSQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLD 445

Query: 430 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI 489
           LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+
Sbjct: 446 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 505

Query: 490 SRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 549
            R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFI
Sbjct: 506 VRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFI 565

Query: 550 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT 609
           ED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VT
Sbjct: 566 EDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVT 625

Query: 610 RERIRQIEAKALRKLR 625
           RERIRQIEAKALRKL+
Sbjct: 626 RERIRQIEAKALRKLK 641


>gi|103486468|ref|YP_616029.1| RNA polymerase sigma factor RpoD [Sphingopyxis alaskensis RB2256]
 gi|98976545|gb|ABF52696.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingopyxis alaskensis
            RB2256]
          Length = 669

 Score =  507 bits (1306), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 291/656 (44%), Positives = 399/656 (60%), Gaps = 70/656 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  GK+RGYLT+ E+N  LP+D +  E IE I+     M I++ E   D +      
Sbjct: 22   KKLIARGKKRGYLTYDELNAALPQDEMSSEQIEDIMSAISDMGINIVESDEDVQEEAEQE 81

Query: 894  ITSDDDVEEAT--------EAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
            +  + DV   T        E    TVD    RT DP++MY+REMG+VELL+R+GEI IAK
Sbjct: 82   VDDEVDVSAGTGSVSNPAIEKKKETVD----RTDDPVRMYLREMGAVELLSREGEIAIAK 137

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKG 1003
            RIE G   MI  +   P T   I+  ++ ++  ++++ EIVD   ++ K+ +  N   +G
Sbjct: 138  RIEAGRDTMILGLCESPLTFNAIIEWSNALNNGDMQLREIVDLEAMLSKDPAPENLDEEG 197

Query: 1004 NKNNN-----------EEKILIESSSAD------------------------LSTEQLEK 1028
             ++             +E  + E  +AD                        LS   +E+
Sbjct: 198  AEDGEISEKTAGVSFKDEDEVEEEPAADGDDEDGEGTSGKRESFDDDDEDNTLSLAAMEE 257

Query: 1029 L-KYESLIKFSNISFHFDKMRKAFEK---------------EGYNSESYIKAHNNISNEM 1072
            L K ++L KF+NI+  F    KAF+K                  + + Y K    ++ ++
Sbjct: 258  LLKPDALEKFANITKSF----KAFQKLQEARLEALSSGEEFPAASEKKYHKLREELTAQV 313

Query: 1073 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 1132
              ++F    IE L D L +   ++T +  Q+L +   +  +PR  F+  +   E+  NW+
Sbjct: 314  ESVQFHGTKIEYLVDQLYSYNRRLTALGGQMLRLA-ERHKVPRKSFLDHYVGRELEENWL 372

Query: 1133 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 1192
            +    I   +         ++  ++ ++  +     + L + R +   +  GE +AR AK
Sbjct: 373  EEVAGIDKKWAAFAENEAAAVDRIRVEISEIAQAAGMSLTEFRRVVNMVQKGEREARIAK 432

Query: 1193 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252
            +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 433  KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 492

Query: 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 1312
            QAITRSIADQARTIRIPVHMIETINK+ R SRQ L E+G EP P  +A ++ MP EK+RK
Sbjct: 493  QAITRSIADQARTIRIPVHMIETINKLVRCSRQFLHESGREPTPEEMAERLSMPLEKVRK 552

Query: 1313 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 1372
            +MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ ++++  V  +L SLTPRE 
Sbjct: 553  VMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPVDAAVQSNLKETVTRVLASLTPREE 612

Query: 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 613  RVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 668



 Score =  491 bits (1263), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 284/643 (44%), Positives = 389/643 (60%), Gaps = 70/643 (10%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  GK+RGYLT+ E+N  LP+D +  E IE I+     M I++ E   D +      
Sbjct: 22  KKLIARGKKRGYLTYDELNAALPQDEMSSEQIEDIMSAISDMGINIVESDEDVQEEAEQE 81

Query: 104 ITSDDDVEEAT--------EAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
           +  + DV   T        E    TVD    RT DP++MY+REMG+VELL+R+GEI IAK
Sbjct: 82  VDDEVDVSAGTGSVSNPAIEKKKETVD----RTDDPVRMYLREMGAVELLSREGEIAIAK 137

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKG 213
           RIE G   MI  +   P T   I+  ++ ++  ++++ EIVD   ++ K+ +  N   +G
Sbjct: 138 RIEAGRDTMILGLCESPLTFNAIIEWSNALNNGDMQLREIVDLEAMLSKDPAPENLDEEG 197

Query: 214 NKNNN-----------EEKILIESSSAD------------------------LSTEQLEK 238
            ++             +E  + E  +AD                        LS   +E+
Sbjct: 198 AEDGEISEKTAGVSFKDEDEVEEEPAADGDDEDGEGTSGKRESFDDDDEDNTLSLAAMEE 257

Query: 239 L-KYESLIKFSNISFHFDKMRKAFEK---------------EGYNSESYIKAHNNISNEM 282
           L K ++L KF+NI+  F    KAF+K                  + + Y K    ++ ++
Sbjct: 258 LLKPDALEKFANITKSF----KAFQKLQEARLEALSSGEEFPAASEKKYHKLREELTAQV 313

Query: 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWV 342
             ++F    IE L D L +   ++T +  Q+L +   +  +PR  F+  +   E+  NW+
Sbjct: 314 ESVQFHGTKIEYLVDQLYSYNRRLTALGGQMLRLA-ERHKVPRKSFLDHYVGRELEENWL 372

Query: 343 DNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           +    I   +         ++  ++ ++  +     + L + R +   +  GE +AR AK
Sbjct: 373 EEVAGIDKKWAAFAENEAAAVDRIRVEISEIAQAAGMSLTEFRRVVNMVQKGEREARIAK 432

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 433 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 492

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIADQARTIRIPVHMIETINK+ R SRQ L E+G EP P  +A ++ MP EK+RK
Sbjct: 493 QAITRSIADQARTIRIPVHMIETINKLVRCSRQFLHESGREPTPEEMAERLSMPLEKVRK 552

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           +MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ ++++  V  +L SLTPRE 
Sbjct: 553 VMKIAKEPISLETPIGDEEDSHLGDFIEDKNAVIPVDAAVQSNLKETVTRVLASLTPREE 612

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 613 RVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|167829080|ref|ZP_02460551.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia pseudomallei 9]
          Length = 285

 Score =  507 bits (1306), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 239/284 (84%), Positives = 268/284 (94%)

Query: 1146 LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
            + RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVIS
Sbjct: 1    MSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 60

Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
            IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 61   IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 120

Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 1325
            IRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+
Sbjct: 121  IRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMET 180

Query: 1326 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 1385
            P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+
Sbjct: 181  PIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMST 240

Query: 1386 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429
            DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR  KLK FLEG
Sbjct: 241  DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSDKLKSFLEG 284



 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 228/270 (84%), Positives = 257/270 (95%)

Query: 356 LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
           + RNIP+I+E QQ+L++LQ  +VLPL DL++ NR+M AGE+KAR+AKREMTEANLRLVIS
Sbjct: 1   MSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 60

Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
           IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 61  IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 120

Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535
           IRIPVHMIETINK++RISRQILQETG EPDP+ +A KMEMPE+KIRKIMKIAKEP+SME+
Sbjct: 121 IRIPVHMIETINKMNRISRQILQETGLEPDPATLAEKMEMPEDKIRKIMKIAKEPISMET 180

Query: 536 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 595
           P+GDD+DSHLGDFIED N +AP+DAAL+ASMR VVKD+L+SLTPRE+KVLRMRFGIEMS+
Sbjct: 181 PIGDDDDSHLGDFIEDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMST 240

Query: 596 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 241 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 270


>gi|365855655|ref|ZP_09395698.1| RNA polymerase sigma factor RpoD [Acetobacteraceae bacterium AT-5844]
 gi|363718963|gb|EHM02284.1| RNA polymerase sigma factor RpoD [Acetobacteraceae bacterium AT-5844]
          Length = 639

 Score =  507 bits (1305), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 288/641 (44%), Positives = 393/641 (61%), Gaps = 23/641 (3%)

Query: 808  FSKKNAFSFDIKSNSREEIEN-----LRKKFKILIKLGKERGYLTFSEINDFLPEDIIDH 862
             + K A   +   N  E +E      L    K L+  GKERGY+T+ E+N  LP + +  
Sbjct: 1    MASKTAGGTETVENRDEAVEGALLDTLSAAVKKLVARGKERGYVTYDELNAALPSEQVSS 60

Query: 863  EIIESIIKTFRYMDISV--SEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKD 920
            E+IE  +     + I+V  SE   D E    +     +D E   E   +  +   GRT D
Sbjct: 61   ELIEDTMAMLSELGINVVESEEAEDGEGKAPAKAEGAEDEESEEEEGGNVNEESLGRTDD 120

Query: 921  PIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEI 980
            P++MY+REMGSVELL+R+GEI IAKRIE G   MI  +   P T   IL   + I    +
Sbjct: 121  PVRMYLREMGSVELLSREGEIAIAKRIEAGRDAMIGGLCESPLTFQAILTWHEAIKDGRM 180

Query: 981  KIDEIVDGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSN 1039
             + +++D  ++   ++++  +       E +   E     LS   LE KLK E+L  F  
Sbjct: 181  LLRDVID--LEATAAADSPDVPPPSEAEEFEEGEEGEGMGLSLSALEEKLKPEALATFEE 238

Query: 1040 ISFHFDKMRK-------AFEKEGYNSESYIKAHNNISNEMLG----IRFTAKSIEKLCDT 1088
            I   + K+ K       A+   G       +A+  + +E++     ++     IE+L D 
Sbjct: 239  IESLYGKLHKMQLKRMEAYTAGGGLGSKTEQAYETLRSELVAAVEKVQLHNNRIEELVDQ 298

Query: 1089 LRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILC 1147
            L+    ++T  E QIL +      + R  F+  +   EI+  W D  + +    +   + 
Sbjct: 299  LKGLNRRITGFEGQILRLA-EASKVKRDDFLNHWVGAEIDPAWFDRVSNLSGKAWKTFVE 357

Query: 1148 RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIA 1207
            R+   ++ +++++        LP+N+ + +   +  GE    +AK+EM EANLRLVISIA
Sbjct: 358  RSRDEVEAIRKQIGATAEVTGLPVNEFKRVYSAVSRGERDMTQAKKEMIEANLRLVISIA 417

Query: 1208 KKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 1267
            KKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR
Sbjct: 418  KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 477

Query: 1268 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327
            IPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+
Sbjct: 478  IPVHMIETINKLVRTSRQMLHEIGREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPI 537

Query: 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387
            GD+EDSHLGDFIED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DH
Sbjct: 538  GDEEDSHLGDFIEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDH 597

Query: 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 598  TLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 638



 Score =  489 bits (1260), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 275/605 (45%), Positives = 377/605 (62%), Gaps = 18/605 (2%)

Query: 36  IENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHV 93
           ++ L    K L+  GKERGY+T+ E+N  LP + +  E+IE  +     + I+V  SE  
Sbjct: 24  LDTLSAAVKKLVARGKERGYVTYDELNAALPSEQVSSELIEDTMAMLSELGINVVESEEA 83

Query: 94  LDTETLMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
            D E    +     +D E   E   +  +   GRT DP++MY+REMGSVELL+R+GEI I
Sbjct: 84  EDGEGKAPAKAEGAEDEESEEEEGGNVNEESLGRTDDPVRMYLREMGSVELLSREGEIAI 143

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKG 213
           AKRIE G   MI  +   P T   IL   + I    + + +++D  ++   ++++  +  
Sbjct: 144 AKRIEAGRDAMIGGLCESPLTFQAILTWHEAIKDGRMLLRDVID--LEATAAADSPDVPP 201

Query: 214 NKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK-------AFEKEG 265
                E +   E     LS   LE KLK E+L  F  I   + K+ K       A+   G
Sbjct: 202 PSEAEEFEEGEEGEGMGLSLSALEEKLKPEALATFEEIESLYGKLHKMQLKRMEAYTAGG 261

Query: 266 YNSESYIKAHNNISNEMLG----IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKC 321
                  +A+  + +E++     ++     IE+L D L+    ++T  E QIL +     
Sbjct: 262 GLGSKTEQAYETLRSELVAAVEKVQLHNNRIEELVDQLKGLNRRITGFEGQILRLA-EAS 320

Query: 322 GMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQKLINLQTDIVLP 380
            + R  F+  +   EI+  W D  + +    +   + R+   ++ +++++        LP
Sbjct: 321 KVKRDDFLNHWVGAEIDPAWFDRVSNLSGKAWKTFVERSRDEVEAIRKQIGATAEVTGLP 380

Query: 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 440
           +N+ + +   +  GE    +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMK
Sbjct: 381 VNEFKRVYSAVSRGERDMTQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 440

Query: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET 500
           AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ R SRQ+L E 
Sbjct: 441 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEI 500

Query: 501 GSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560
           G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+  + P DA
Sbjct: 501 GREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKAAVIPLDA 560

Query: 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620
           A+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTRERIRQIEAKA
Sbjct: 561 AIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKA 620

Query: 621 LRKLR 625
           LRKL+
Sbjct: 621 LRKLK 625


>gi|58038783|ref|YP_190747.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
 gi|58001197|gb|AAW60091.1| RNA polymerase sigma factor RpoD [Gluconobacter oxydans 621H]
          Length = 652

 Score =  506 bits (1304), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 284/622 (45%), Positives = 396/622 (63%), Gaps = 27/622 (4%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LI  G+ERG++TF E+N  LP+D +  E IE ++     M I V E+    E    +
Sbjct: 30   VKRLIAKGRERGHITFDELNAVLPQDQMSSEQIEDVMAALSEMGIQVIENEDQDEAEAPA 89

Query: 893  NITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
               ++ D EEA       VD++   RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 90   EKEAEGDGEEAEGPQGGNVDAEAASRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 149

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN--NE 1009
             +MI  +   P TI  I+   +++   E+ + +IVD    +    +   ++G + +  +E
Sbjct: 150  DEMIGGLCESPLTIRAIISWHERLKDGEMLLRDIVDLEASQGGGPDPEAVEGEEGDEASE 209

Query: 1010 E----------KILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK--------- 1049
            E              +   + LS   LE KLK E L +F  I   + K+RK         
Sbjct: 210  EDDTAEDENEEGEGDQQEGSGLSLSALEEKLKPEILARFEAIEPLYHKLRKLQIKRIEAL 269

Query: 1050 -AFEKEGYNSE-SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 1107
               E     SE +Y K  + + + +  +      IE+L   ++ Q+ ++  +E +++ + 
Sbjct: 270  TGGEDHSDKSEQTYEKLRHELVSLVEQVHLHNNRIEELVAQIKMQVQKLNNVEGRMMRLA 329

Query: 1108 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTD 1166
               C + R  F+  +   E++  W+D+ + +    +  +  +++  ++ L+ ++  L  +
Sbjct: 330  -ESCKISRDDFLIKYRSRELDPTWLDSISALPGKGWKNLTTKHMDQLRNLRGEIAALSHE 388

Query: 1167 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226
              LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 389  TGLPVGEFRRVYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 448

Query: 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 1286
            GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA+TIRIPVHMIETINK+ R SRQ+
Sbjct: 449  GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRTSRQM 508

Query: 1287 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346
            L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+  + 
Sbjct: 509  LHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVI 568

Query: 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406
            P DAA+  ++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTRERIRQI
Sbjct: 569  PLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQI 628

Query: 1407 EAKALRKLRHPSRYYKLKIFLE 1428
            EAKALRKL+HPSR  KL+ FL+
Sbjct: 629  EAKALRKLKHPSRSRKLRSFLD 650



 Score =  489 bits (1259), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 276/609 (45%), Positives = 386/609 (63%), Gaps = 27/609 (4%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K LI  G+ERG++TF E+N  LP+D +  E IE ++     M I V E+    E    +
Sbjct: 30  VKRLIAKGRERGHITFDELNAVLPQDQMSSEQIEDVMAALSEMGIQVIENEDQDEAEAPA 89

Query: 103 NITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
              ++ D EEA       VD++   RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 90  EKEAEGDGEEAEGPQGGNVDAEAASRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 149

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN--NE 219
            +MI  +   P TI  I+   +++   E+ + +IVD    +    +   ++G + +  +E
Sbjct: 150 DEMIGGLCESPLTIRAIISWHERLKDGEMLLRDIVDLEASQGGGPDPEAVEGEEGDEASE 209

Query: 220 E----------KILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK--------- 259
           E              +   + LS   LE KLK E L +F  I   + K+RK         
Sbjct: 210 EDDTAEDENEEGEGDQQEGSGLSLSALEEKLKPEILARFEAIEPLYHKLRKLQIKRIEAL 269

Query: 260 -AFEKEGYNSE-SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIV 317
              E     SE +Y K  + + + +  +      IE+L   ++ Q+ ++  +E +++ + 
Sbjct: 270 TGGEDHSDKSEQTYEKLRHELVSLVEQVHLHNNRIEELVAQIKMQVQKLNNVEGRMMRLA 329

Query: 318 VNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTD 376
              C + R  F+  +   E++  W+D+ + +    +  +  +++  ++ L+ ++  L  +
Sbjct: 330 -ESCKISRDDFLIKYRSRELDPTWLDSISALPGKGWKNLTTKHMDQLRNLRGEIAALSHE 388

Query: 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 436
             LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNI
Sbjct: 389 TGLPVGEFRRVYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 448

Query: 437 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQI 496
           GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA+TIRIPVHMIETINK+ R SRQ+
Sbjct: 449 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRTSRQM 508

Query: 497 LQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLA 556
           L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+  + 
Sbjct: 509 LHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVI 568

Query: 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616
           P DAA+  ++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTRERIRQI
Sbjct: 569 PLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQI 628

Query: 617 EAKALRKLR 625
           EAKALRKL+
Sbjct: 629 EAKALRKLK 637


>gi|330993917|ref|ZP_08317847.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
 gi|329758863|gb|EGG75377.1| RNA polymerase sigma factor rpoD [Gluconacetobacter sp. SXCC-1]
          Length = 659

 Score =  506 bits (1304), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 293/628 (46%), Positives = 394/628 (62%), Gaps = 34/628 (5%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 891
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    DTE    
Sbjct: 31   KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDDTEAAAT 90

Query: 892  SNITSDDDVEEATEA---ALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            ++   DD  EE +E+   A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91   ADTKGDDTAEEESESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD------GLIDKN-------- 993
            E G  +MI  +   P T   I+   +++   E+ + +IVD      G  D          
Sbjct: 151  EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGGNDPAEAVEGEDA 210

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK--A 1050
            F+ N+          E +   E   A LS   LE KLK E L +F  +   ++ + +  A
Sbjct: 211  FAENDGNEAEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFKEVEALYEALHRVQA 270

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQIEK 1101
               E + + S I A      E L +    K          IE L + L+    ++  +E 
Sbjct: 271  ERLEKFTAGSDISAEEESRYEQLRLELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGLEG 330

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKL 1160
            ++L +      + R  F+  +   E++  W+D    +    +   + ++  ++  L+ ++
Sbjct: 331  RMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVIRLRNQV 389

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
             +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 390  ADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 449

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ 
Sbjct: 450  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 509

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 510  RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 569

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTR
Sbjct: 570  DKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 629

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 630  ERIRQIEAKALRKLKHPSRSRKLRSFLD 657



 Score =  489 bits (1259), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 285/615 (46%), Positives = 384/615 (62%), Gaps = 34/615 (5%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 101
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    DTE    
Sbjct: 31  KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDDTEAAAT 90

Query: 102 SNITSDDDVEEATEA---ALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           ++   DD  EE +E+   A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91  ADTKGDDTAEEESESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD------GLIDKN-------- 203
           E G  +MI  +   P T   I+   +++   E+ + +IVD      G  D          
Sbjct: 151 EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGGNDPAEAVEGEDA 210

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK--A 260
           F+ N+          E +   E   A LS   LE KLK E L +F  +   ++ + +  A
Sbjct: 211 FAENDGNEAEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFKEVEALYEALHRVQA 270

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQIEK 311
              E + + S I A      E L +    K          IE L + L+    ++  +E 
Sbjct: 271 ERLEKFTAGSDISAEEESRYEQLRLELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGLEG 330

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKL 370
           ++L +      + R  F+  +   E++  W+D    +    +   + ++  ++  L+ ++
Sbjct: 331 RMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVIRLRNQV 389

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
            +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 390 ADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 449

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ 
Sbjct: 450 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 509

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 510 RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 569

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTR
Sbjct: 570 DKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 629

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKL+
Sbjct: 630 ERIRQIEAKALRKLK 644


>gi|349699310|ref|ZP_08900939.1| RNA polymerase sigma factor RpoD [Gluconacetobacter europaeus LMG
            18494]
          Length = 659

 Score =  506 bits (1303), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 294/630 (46%), Positives = 394/630 (62%), Gaps = 38/630 (6%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 891
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    +TET   
Sbjct: 31   KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDETETPAP 90

Query: 892  SNITSDDDVEEATE---AALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
            +   SDD  EE +E    A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91   AETKSDDTAEEESESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            E G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S  N  ++  +  
Sbjct: 151  EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGNDPVEATEGE 208

Query: 1008 N----------------EEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK- 1049
                             E +   E   A LS   LE KLK E L +F  +   +D + + 
Sbjct: 209  EAFGENEGAENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYDALHRV 268

Query: 1050 -AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQI 1099
             A   E + +   I A +    E L +    K          IE L + L+    ++  +
Sbjct: 269  QAERLEKFTAGEEISADDESRYEQLRMELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGL 328

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPSIKELQQ 1158
            E ++L +      + R  F+  +   E++  W+D   T     +   L ++  ++  L+ 
Sbjct: 329  EGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWIDMVATLPAKSWKNFLAKHGETVIRLRN 387

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            ++  L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 388  QVAELTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFL 447

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 448  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 507

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            + R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 508  LVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 567

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+V
Sbjct: 568  IEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNV 627

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 628  TRERIRQIEAKALRKLKHPSRSRKLRSFLD 657



 Score =  489 bits (1258), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 286/617 (46%), Positives = 384/617 (62%), Gaps = 38/617 (6%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 101
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    +TET   
Sbjct: 31  KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDETETPAP 90

Query: 102 SNITSDDDVEEATE---AALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
           +   SDD  EE +E    A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91  AETKSDDTAEEESESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           E G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S  N  ++  +  
Sbjct: 151 EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGNDPVEATEGE 208

Query: 218 N----------------EEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK- 259
                            E +   E   A LS   LE KLK E L +F  +   +D + + 
Sbjct: 209 EAFGENEGAENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYDALHRV 268

Query: 260 -AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQI 309
            A   E + +   I A +    E L +    K          IE L + L+    ++  +
Sbjct: 269 QAERLEKFTAGEEISADDESRYEQLRMELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGL 328

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPSIKELQQ 368
           E ++L +      + R  F+  +   E++  W+D   T     +   L ++  ++  L+ 
Sbjct: 329 EGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWIDMVATLPAKSWKNFLAKHGETVIRLRN 387

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           ++  L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 388 QVAELTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFL 447

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 448 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 507

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           + R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 508 LVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 567

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+V
Sbjct: 568 IEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNV 627

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKL+
Sbjct: 628 TRERIRQIEAKALRKLK 644


>gi|383645191|ref|ZP_09957597.1| RNA polymerase sigma factor RpoD [Sphingomonas elodea ATCC 31461]
          Length = 675

 Score =  506 bits (1303), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 289/657 (43%), Positives = 402/657 (61%), Gaps = 71/657 (10%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K L+   K+RGY+T  ++N+ LP+D +  E IE ++     M I+V E+    E     
Sbjct: 28   IKKLVARAKKRGYITVDQLNEMLPQDQMSSEQIEDVMAALNDMGINVVENEDAGE----- 82

Query: 893  NITSDDDVEEATEAALSTVDS-----------DFGRTKDPIKMYMREMGSVELLTRDGEI 941
            +  S+DD  +  E A S+ DS              RT DP++MY+REMG+VELL+R+GEI
Sbjct: 83   DAESEDDSADDAETADSSDDSAPAFEIAKKKETVDRTDDPVRMYLREMGAVELLSREGEI 142

Query: 942  EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNR 999
             IAKRIE G   MI  +   P T   I+  +  +++  +++ EI+D   ++ K  S+   
Sbjct: 143  AIAKRIEAGRDTMILGLCESPITFNAIIGWSTALNEGTMQLREILDLDAMLSKGPSAEQ- 201

Query: 1000 VIKGNKNNNEEKILIESSSA------------------------------------DLST 1023
             ++G +++N E  + ESS+                                      LS 
Sbjct: 202  -VEGAEDDNGE--ISESSTGPSFKEEEEPEEVASDEDDELTERRARRPSDDEEEDNTLSL 258

Query: 1024 EQLE-KLKYESLIKFSNISFHFDKMRKAFEKE-----------GYNSESYIKAHNNISNE 1071
             Q+E +LK ++L KF+NI+  + K  K  ++                + Y K    ++ E
Sbjct: 259  AQMEEQLKPQALEKFANITAIYKKFSKVQQQRLDTMSAGEDFPAAEEKKYNKLREELTAE 318

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
            +  ++F    IE L D L +   ++T +  Q+L +   +  + R  F+  + ++E++ NW
Sbjct: 319  VESVQFHQAKIEYLVDQLYSFNRRLTALGGQMLRLA-ERHKVSRKDFLDRYVDHELDENW 377

Query: 1132 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 1191
            + +   I   +   +     S+  ++ ++  +     + L + R I   +  GE +AR A
Sbjct: 378  LPSVVGIDKKWKNFVENESSSVDRIRTEMSEIAQQTGMTLTEFRRIVNMVQKGEREARIA 437

Query: 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251
            K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 438  KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 497

Query: 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 1311
            RQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+R
Sbjct: 498  RQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVR 557

Query: 1312 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
            K+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE
Sbjct: 558  KVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPRE 617

Query: 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 618  ERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 674



 Score =  489 bits (1259), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 282/644 (43%), Positives = 392/644 (60%), Gaps = 71/644 (11%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K L+   K+RGY+T  ++N+ LP+D +  E IE ++     M I+V E+    E     
Sbjct: 28  IKKLVARAKKRGYITVDQLNEMLPQDQMSSEQIEDVMAALNDMGINVVENEDAGE----- 82

Query: 103 NITSDDDVEEATEAALSTVDS-----------DFGRTKDPIKMYMREMGSVELLTRDGEI 151
           +  S+DD  +  E A S+ DS              RT DP++MY+REMG+VELL+R+GEI
Sbjct: 83  DAESEDDSADDAETADSSDDSAPAFEIAKKKETVDRTDDPVRMYLREMGAVELLSREGEI 142

Query: 152 EIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNR 209
            IAKRIE G   MI  +   P T   I+  +  +++  +++ EI+D   ++ K  S+   
Sbjct: 143 AIAKRIEAGRDTMILGLCESPITFNAIIGWSTALNEGTMQLREILDLDAMLSKGPSAEQ- 201

Query: 210 VIKGNKNNNEEKILIESSSA------------------------------------DLST 233
            ++G +++N E  + ESS+                                      LS 
Sbjct: 202 -VEGAEDDNGE--ISESSTGPSFKEEEEPEEVASDEDDELTERRARRPSDDEEEDNTLSL 258

Query: 234 EQLE-KLKYESLIKFSNISFHFDKMRKAFEKE-----------GYNSESYIKAHNNISNE 281
            Q+E +LK ++L KF+NI+  + K  K  ++                + Y K    ++ E
Sbjct: 259 AQMEEQLKPQALEKFANITAIYKKFSKVQQQRLDTMSAGEDFPAAEEKKYNKLREELTAE 318

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           +  ++F    IE L D L +   ++T +  Q+L +   +  + R  F+  + ++E++ NW
Sbjct: 319 VESVQFHQAKIEYLVDQLYSFNRRLTALGGQMLRLA-ERHKVSRKDFLDRYVDHELDENW 377

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
           + +   I   +   +     S+  ++ ++  +     + L + R I   +  GE +AR A
Sbjct: 378 LPSVVGIDKKWKNFVENESSSVDRIRTEMSEIAQQTGMTLTEFRRIVNMVQKGEREARIA 437

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 438 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 497

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+R
Sbjct: 498 RQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVR 557

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           K+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE
Sbjct: 558 KVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPRE 617

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 618 ERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 661


>gi|295690890|ref|YP_003594583.1| RNA polymerase sigma 70 factor subunit RpoD [Caulobacter segnis ATCC
            21756]
 gi|295432793|gb|ADG11965.1| RNA polymerase, sigma 70 subunit, RpoD [Caulobacter segnis ATCC
            21756]
          Length = 652

 Score =  506 bits (1303), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 286/631 (45%), Positives = 394/631 (62%), Gaps = 42/631 (6%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            KKF   IK  K RGY+T  E+N  LP + +  + IE  +     M ++V E   D E   
Sbjct: 30   KKF---IKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAEGGE 86

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
               + + D   E T    S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87   GGEVATRD---ENTTVITSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
               MI  +     T   I++  +++    I + E++D  ++  +++ N V       +EE
Sbjct: 144  RDTMIRGLCESALTFEAIMVWREELGSGRILLREVID--LEGTYAAINGVAAQPAAEDEE 201

Query: 1011 KIL--IESSSADLSTEQLE--------------------KLKYESLIKFSNISFHFDKMR 1048
                 I+  + +   E  E                    +L+   +     I+  F+  R
Sbjct: 202  GPAEPIDDEAGEAKPEGAEGEDDDDFDDGAGPTVSAMEGELREGVMAILDAIASEFESFR 261

Query: 1049 KAFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVT 1097
            K  +K      +G + SE+  KA+  +S  ++     ++     IE L + L     ++ 
Sbjct: 262  KLQDKLVGSRLKGEDLSEADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLI 321

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
             +E ++L +  +  G+ R  F+K +  +E+N  W +    +   +   +  +  SI +++
Sbjct: 322  GLEGRLLRLA-DSYGISRAEFLKAYFGSELNPTWGEQVKAMGVRWTKFVENDNSSISDIR 380

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
            Q++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 381  QEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 440

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 441  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 500

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 501  KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 560

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 561  FIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 620

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 621  VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 651



 Score =  489 bits (1258), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 278/618 (44%), Positives = 384/618 (62%), Gaps = 42/618 (6%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           KKF   IK  K RGY+T  E+N  LP + +  + IE  +     M ++V E   D E   
Sbjct: 30  KKF---IKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAEGGE 86

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
              + + D   E T    S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 87  GGEVATRD---ENTTVITSDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 143

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
              MI  +     T   I++  +++    I + E++D  ++  +++ N V       +EE
Sbjct: 144 RDTMIRGLCESALTFEAIMVWREELGSGRILLREVID--LEGTYAAINGVAAQPAAEDEE 201

Query: 221 KIL--IESSSADLSTEQLE--------------------KLKYESLIKFSNISFHFDKMR 258
                I+  + +   E  E                    +L+   +     I+  F+  R
Sbjct: 202 GPAEPIDDEAGEAKPEGAEGEDDDDFDDGAGPTVSAMEGELREGVMAILDAIASEFESFR 261

Query: 259 KAFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVT 307
           K  +K      +G + SE+  KA+  +S  ++     ++     IE L + L     ++ 
Sbjct: 262 KLQDKLVGSRLKGEDLSEADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLI 321

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
            +E ++L +  +  G+ R  F+K +  +E+N  W +    +   +   +  +  SI +++
Sbjct: 322 GLEGRLLRLA-DSYGISRAEFLKAYFGSELNPTWGEQVKAMGVRWTKFVENDNSSISDIR 380

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
           Q++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 381 QEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 440

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 441 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 500

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 501 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 560

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 561 FIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 620

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKL+
Sbjct: 621 VTRERIRQIEAKALRKLK 638


>gi|260753821|ref|YP_003226714.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
            NCIMB 11163]
 gi|258553184|gb|ACV76130.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
            mobilis NCIMB 11163]
          Length = 671

 Score =  506 bits (1303), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 290/645 (44%), Positives = 398/645 (61%), Gaps = 55/645 (8%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE------TL 889
             I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+    E        
Sbjct: 29   FITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEED 88

Query: 890  MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
                +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE 
Sbjct: 89   AAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEA 146

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKNN 1007
            G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +    +G+ N+
Sbjct: 147  GRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEEGDDND 206

Query: 1008 NE----------------------------EKI----LIESSSADLSTEQLE-KLKYESL 1034
            NE                            ++I    + E     LS  Q+E +LK  SL
Sbjct: 207  NEISERNAGPTFKEDDDEDDDSEGELDENGQRIQRENMDEEDENTLSLAQMEEQLKPASL 266

Query: 1035 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 1083
             KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267  EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 1084 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 1143
             L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327  FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                    SI+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386  NFTTSEAESIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506  RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566  ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 626  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 670



 Score =  489 bits (1260), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 388/632 (61%), Gaps = 55/632 (8%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE------TL 99
            I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+    E        
Sbjct: 29  FITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEED 88

Query: 100 MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
               +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE 
Sbjct: 89  AAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEA 146

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKNN 217
           G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +    +G+ N+
Sbjct: 147 GRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEEGDDND 206

Query: 218 NE----------------------------EKI----LIESSSADLSTEQLE-KLKYESL 244
           NE                            ++I    + E     LS  Q+E +LK  SL
Sbjct: 207 NEISERNAGPTFKEDDDEDDDSEGELDENGQRIQRENMDEEDENTLSLAQMEEQLKPASL 266

Query: 245 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 293
            KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267 EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 294 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 353
            L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327 FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
                   SI+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386 NFTTSEAESIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506 RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566 ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 626 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|397677341|ref|YP_006518879.1| RNA polymerase sigma-70 subunit RpoD [Zymomonas mobilis subsp.
            mobilis ATCC 29191]
 gi|395398030|gb|AFN57357.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
            mobilis ATCC 29191]
          Length = 671

 Score =  506 bits (1302), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 290/645 (44%), Positives = 398/645 (61%), Gaps = 55/645 (8%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH-------VLDTET 888
             I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+         + E 
Sbjct: 29   FITQAKKRGYITYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEEE 88

Query: 889  LMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 948
                 +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE
Sbjct: 89   DAAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIE 146

Query: 949  EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKN 1006
             G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +     G+ N
Sbjct: 147  AGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEDGDDN 206

Query: 1007 NNE----------------------------EKILIESSSAD---LSTEQLE-KLKYESL 1034
            +NE                            ++I  E+   D   LS  Q+E +LK  SL
Sbjct: 207  DNEISERNAGPTFKEDDEDEDDSEGELDENGQRIQRENEEEDENTLSLAQMEEQLKPASL 266

Query: 1035 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 1083
             KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267  EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 1084 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 1143
             L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327  FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                     I+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386  NFTTSEAEGIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506  RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566  ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 626  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 670



 Score =  489 bits (1260), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 388/632 (61%), Gaps = 55/632 (8%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH-------VLDTET 98
            I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+         + E 
Sbjct: 29  FITQAKKRGYITYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEEE 88

Query: 99  LMLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIE 158
                +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE
Sbjct: 89  DAAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIE 146

Query: 159 EGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKN 216
            G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +     G+ N
Sbjct: 147 AGRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEDGDDN 206

Query: 217 NNE----------------------------EKILIESSSAD---LSTEQLE-KLKYESL 244
           +NE                            ++I  E+   D   LS  Q+E +LK  SL
Sbjct: 207 DNEISERNAGPTFKEDDEDEDDSEGELDENGQRIQRENEEEDENTLSLAQMEEQLKPASL 266

Query: 245 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 293
            KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267 EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 294 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 353
            L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327 FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
                    I+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386 NFTTSEAEGIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506 RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566 ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 626 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|258542087|ref|YP_003187520.1| RNA polymerase sigma factor RpoD [Acetobacter pasteurianus IFO
            3283-01]
 gi|384042008|ref|YP_005480752.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-12]
 gi|384050523|ref|YP_005477586.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-03]
 gi|384053633|ref|YP_005486727.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-07]
 gi|384056865|ref|YP_005489532.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-22]
 gi|384059506|ref|YP_005498634.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-26]
 gi|384062800|ref|YP_005483442.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-32]
 gi|384118876|ref|YP_005501500.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-01-42C]
 gi|256633165|dbj|BAH99140.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-01]
 gi|256636222|dbj|BAI02191.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-03]
 gi|256639277|dbj|BAI05239.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-07]
 gi|256642331|dbj|BAI08286.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-22]
 gi|256645386|dbj|BAI11334.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-26]
 gi|256648441|dbj|BAI14382.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-32]
 gi|256651494|dbj|BAI17428.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-01-42C]
 gi|256654485|dbj|BAI20412.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus IFO 3283-12]
          Length = 672

 Score =  505 bits (1301), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 290/649 (44%), Positives = 390/649 (60%), Gaps = 70/649 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 38   KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 86

Query: 894  ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 929
               D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 87   --EDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 144

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 145  GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 202

Query: 990  IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 1031
            ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 203  LEAMQSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 262

Query: 1032 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
            E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 263  EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 322

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 1139
             IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 323  RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 381

Query: 1140 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 1199
              +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 382  RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 441

Query: 1200 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 1259
            LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 442  LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 501

Query: 1260 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 1319
            ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 502  ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 561

Query: 1320 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 1379
            P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 562  PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 621

Query: 1380 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 622  GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670



 Score =  488 bits (1255), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 282/636 (44%), Positives = 380/636 (59%), Gaps = 70/636 (11%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 38  KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 86

Query: 104 ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 139
              D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 87  --EDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 144

Query: 140 GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 199
           G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 145 GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 202

Query: 200 IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 241
           ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 203 LEAMQSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 262

Query: 242 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
           E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 263 EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 322

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 349
            IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 323 RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 381

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 382 RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 441

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 442 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 501

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 502 ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 561

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 562 PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 621

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 622 GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 657


>gi|56552519|ref|YP_163358.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
            ZM4]
 gi|384412419|ref|YP_005621784.1| RNA polymerase sigma-70 subunit RpoD [Zymomonas mobilis subsp.
            mobilis ATCC 10988]
 gi|56544093|gb|AAV90247.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
            mobilis ZM4]
 gi|335932793|gb|AEH63333.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
            mobilis ATCC 10988]
          Length = 671

 Score =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 290/645 (44%), Positives = 397/645 (61%), Gaps = 55/645 (8%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE------TL 889
             I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+    E        
Sbjct: 29   FITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEED 88

Query: 890  MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
                +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE 
Sbjct: 89   AAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEA 146

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKNN 1007
            G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +     G+ N+
Sbjct: 147  GRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEDGDDND 206

Query: 1008 NE----------------------------EKI----LIESSSADLSTEQLE-KLKYESL 1034
            NE                            ++I    + E     LS  Q+E +LK  SL
Sbjct: 207  NEISERNAGPTFKEDDDEDDDSEGELDENGQRIQRENMDEEDENTLSLAQMEEQLKPASL 266

Query: 1035 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 1083
             KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267  EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 1084 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 1143
             L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327  FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                    SI+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386  NFTTSEAESIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506  RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566  ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 626  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 670



 Score =  489 bits (1258), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 387/632 (61%), Gaps = 55/632 (8%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTE------TL 99
            I   K+RGY+T+ ++N+ LP+D +  E IE I+     M I++ E+    E        
Sbjct: 29  FITQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGINIVENEDSGEDGQQEEED 88

Query: 100 MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
               +  D     A   A++T      RT DP++MY+REMG+VELL+R+GEI IAKRIE 
Sbjct: 89  AAEELQGDGGTSPA--PAITTKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEA 146

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNNRVIKGNKNN 217
           G   MI  +   P T   I+  ++ +++  +++ EI+D   ++ +  S +     G+ N+
Sbjct: 147 GRDTMILGLCESPITFDNIIEWSNALNEGTLQLREIIDLDAMLTQGPSPDQFEEDGDDND 206

Query: 218 NE----------------------------EKI----LIESSSADLSTEQLE-KLKYESL 244
           NE                            ++I    + E     LS  Q+E +LK  SL
Sbjct: 207 NEISERNAGPTFKEDDDEDDDSEGELDENGQRIQRENMDEEDENTLSLAQMEEQLKPASL 266

Query: 245 IKFSNIS---FHFDKMRKAFEKE-GYNSE-------SYIKAHNNISNEMLGIRFTAKSIE 293
            KF+ I+     F  ++ A  +  G N E       +Y +    ++ E+  ++F    IE
Sbjct: 267 EKFAKIADLYRQFSVLQNARMRALGANEEFPEDQENAYQQLREELTAEVESVKFHNARIE 326

Query: 294 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYN 353
            L + L N  +++  +  Q+L +   +  +PR  F+  +  NE+   WV+  +KI   + 
Sbjct: 327 FLVEQLYNYNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGNEMEEGWVERVSKIDKKWA 385

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
                   SI+ ++ ++  +     + L +LR I   +  GE +AR AK EM EANLRLV
Sbjct: 386 NFTTSEAESIERIRSEVAEIAQVTGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLV 445

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 446 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 505

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+
Sbjct: 506 RTIRIPVHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISL 565

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M
Sbjct: 566 ETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGM 625

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 626 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|421848674|ref|ZP_16281661.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus NBRC 101655]
 gi|371460554|dbj|GAB26864.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus NBRC 101655]
          Length = 663

 Score =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 290/649 (44%), Positives = 390/649 (60%), Gaps = 70/649 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 29   KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 77

Query: 894  ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 929
               D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 78   --EDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 135

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 136  GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 193

Query: 990  IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 1031
            ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 194  LEAMQSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 253

Query: 1032 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
            E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 254  EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 313

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 1139
             IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 314  RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 372

Query: 1140 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 1199
              +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 373  RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 432

Query: 1200 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 1259
            LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 433  LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 492

Query: 1260 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 1319
            ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 493  ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 552

Query: 1320 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 1379
            P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 553  PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 612

Query: 1380 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 613  GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 661



 Score =  488 bits (1255), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 282/636 (44%), Positives = 380/636 (59%), Gaps = 70/636 (11%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 29  KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 77

Query: 104 ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 139
              D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 78  --EDNDNEEAEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 135

Query: 140 GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 199
           G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 136 GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 193

Query: 200 IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 241
           ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 194 LEAMQSGGNPLEEGGDGTFNEAESDSESEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 253

Query: 242 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
           E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 254 EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 313

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 349
            IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 314 RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 372

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 373 RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 432

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 433 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 492

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 493 ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 552

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 553 PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 612

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 613 GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 648


>gi|296116667|ref|ZP_06835277.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
            23769]
 gi|295976879|gb|EFG83647.1| RNA polymerase sigma factor RpoD [Gluconacetobacter hansenii ATCC
            23769]
          Length = 659

 Score =  504 bits (1299), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 291/628 (46%), Positives = 392/628 (62%), Gaps = 34/628 (5%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV-LDTET---L 889
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+   D+E+    
Sbjct: 31   KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDSESDDAA 90

Query: 890  MLSNITSDDDVE-EATEAALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                  S++  E ++ E A   VDS+  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91   AEPEAKSEEPAEGDSEEPAAGNVDSENLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKN------------ 993
            E G  +MI  +   P T   I+   +++   E+ + +IVD   +   N            
Sbjct: 151  EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGNAGPGEETEEGEE 210

Query: 994  FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMR--KA 1050
             +S +       N   E+   E   A LS   LE KLK E L +F  +   + ++   +A
Sbjct: 211  PASEDSFDSATDNEESEEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYARLHELQA 270

Query: 1051 FEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQIEK 1101
               E   S   I A    + E L      K          IE L + L+    ++  +E 
Sbjct: 271  TRLEKLTSGGEISAEAEAAYEQLRCELVGKVQQVHLHNTRIEVLVEHLKAIFQRLNGLEG 330

Query: 1102 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQKL 1160
            ++L +      + R  F+  +   E++  WVD  + +    +   + +++ ++  L+ ++
Sbjct: 331  RMLRLA-ESTKVSREDFLLKYRGRELDPGWVDVVSALPGKAWKNFVAKHMETVIRLRGQV 389

Query: 1161 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 1220
              L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 390  AELTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 449

Query: 1221 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 1280
            IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ 
Sbjct: 450  IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 509

Query: 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340
            R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 510  RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 569

Query: 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 1400
            D+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTR
Sbjct: 570  DKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 629

Query: 1401 ERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 630  ERIRQIEAKALRKLKHPSRSRKLRSFLD 657



 Score =  487 bits (1253), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 283/615 (46%), Positives = 382/615 (62%), Gaps = 34/615 (5%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV-LDTET---L 99
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+   D+E+    
Sbjct: 31  KRLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDSESDDAA 90

Query: 100 MLSNITSDDDVE-EATEAALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
                 S++  E ++ E A   VDS+  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91  AEPEAKSEEPAEGDSEEPAAGNVDSENLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKN------------ 203
           E G  +MI  +   P T   I+   +++   E+ + +IVD   +   N            
Sbjct: 151 EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVDLEAMQSGNAGPGEETEEGEE 210

Query: 204 FSSNNRVIKGNKNNNEEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMR--KA 260
            +S +       N   E+   E   A LS   LE KLK E L +F  +   + ++   +A
Sbjct: 211 PASEDSFDSATDNEESEEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYARLHELQA 270

Query: 261 FEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQIEK 311
              E   S   I A    + E L      K          IE L + L+    ++  +E 
Sbjct: 271 TRLEKLTSGGEISAEAEAAYEQLRCELVGKVQQVHLHNTRIEVLVEHLKAIFQRLNGLEG 330

Query: 312 QILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQQKL 370
           ++L +      + R  F+  +   E++  WVD  + +    +   + +++ ++  L+ ++
Sbjct: 331 RMLRLA-ESTKVSREDFLLKYRGRELDPGWVDVVSALPGKAWKNFVAKHMETVIRLRGQV 389

Query: 371 INLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDL 430
             L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDL
Sbjct: 390 AELTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDL 449

Query: 431 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIS 490
           IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ 
Sbjct: 450 IQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLV 509

Query: 491 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550
           R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIE
Sbjct: 510 RTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIE 569

Query: 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTR 610
           D+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTR
Sbjct: 570 DKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTR 629

Query: 611 ERIRQIEAKALRKLR 625
           ERIRQIEAKALRKL+
Sbjct: 630 ERIRQIEAKALRKLK 644


>gi|170744799|ref|YP_001773454.1| RNA polymerase sigma factor RpoD [Methylobacterium sp. 4-46]
 gi|168199073|gb|ACA21020.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium sp. 4-46]
          Length = 666

 Score =  504 bits (1298), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 286/636 (44%), Positives = 394/636 (61%), Gaps = 41/636 (6%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 890
             K +IKL K+RGY+T+ E+N+ LP++    E IE ++     + ++V  +E   D +   
Sbjct: 31   VKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQLSELGVNVVEAEEADDNQAEG 90

Query: 891  LSNITSDDDV--EEATEAA-----------LSTVDSDFGRTKDPIKMYMREMGSVELLTR 937
             +     DD    E TE A             T      RT DP++MY+REMGSVELL+R
Sbjct: 91   AAAEGGGDDEEASEGTEVAEVAPNRPAVLRTETTKEPTDRTDDPVRMYLREMGSVELLSR 150

Query: 938  DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-----GLIDK 992
            +GEI IAKRIE G + MI  +   P T   I+I  D++    + + +I+D        D 
Sbjct: 151  EGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVDGRVLLRDIIDLEATYAGPDG 210

Query: 993  NFSSNNRVIKGNKNNNEEKILIESSSAD-------LSTEQLE-KLKYESLIKFSNISFHF 1044
                    ++   +  E ++       D       +S   +E +LK   L  F  I+ ++
Sbjct: 211  RAGPAEGEVEAEGDGPEGEVAAPEGDGDEDDLENNVSLSAMEAELKPRVLETFDAIAENY 270

Query: 1045 DKMRKA--------FEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 1093
             K+R+          +  G N   S  Y +  + I  ++  +   A  IE L + L +  
Sbjct: 271  RKLRQVQAQQAETRLQGAGANEGQSRQYAELKSRIVADVKSLSLNANRIEALVEQLYDIN 330

Query: 1094 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPS 1152
             ++   E +++ +     G+ R  F++ +   E++ +WV+   K+    +     R    
Sbjct: 331  KRLISQEGRLMRLA-ESHGVARDEFLRHYQGQELDPHWVERVGKLGGKGWKNFTERGQDG 389

Query: 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 1212
            IK L++++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLVISIAKKYT+
Sbjct: 390  IKTLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTN 449

Query: 1213 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272
            RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 450  RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 509

Query: 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332
            IETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+ED
Sbjct: 510  IETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEED 569

Query: 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 1392
            SHLGDFIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEV
Sbjct: 570  SHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 629

Query: 1393 GKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            G+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 630  GQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665



 Score =  487 bits (1253), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 278/623 (44%), Positives = 384/623 (61%), Gaps = 41/623 (6%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 100
            K +IKL K+RGY+T+ E+N+ LP++    E IE ++     + ++V  +E   D +   
Sbjct: 31  VKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQLSELGVNVVEAEEADDNQAEG 90

Query: 101 LSNITSDDDV--EEATEAA-----------LSTVDSDFGRTKDPIKMYMREMGSVELLTR 147
            +     DD    E TE A             T      RT DP++MY+REMGSVELL+R
Sbjct: 91  AAAEGGGDDEEASEGTEVAEVAPNRPAVLRTETTKEPTDRTDDPVRMYLREMGSVELLSR 150

Query: 148 DGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-----GLIDK 202
           +GEI IAKRIE G + MI  +   P T   I+I  D++    + + +I+D        D 
Sbjct: 151 EGEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVDGRVLLRDIIDLEATYAGPDG 210

Query: 203 NFSSNNRVIKGNKNNNEEKILIESSSAD-------LSTEQLE-KLKYESLIKFSNISFHF 254
                   ++   +  E ++       D       +S   +E +LK   L  F  I+ ++
Sbjct: 211 RAGPAEGEVEAEGDGPEGEVAAPEGDGDEDDLENNVSLSAMEAELKPRVLETFDAIAENY 270

Query: 255 DKMRKA--------FEKEGYN---SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQI 303
            K+R+          +  G N   S  Y +  + I  ++  +   A  IE L + L +  
Sbjct: 271 RKLRQVQAQQAETRLQGAGANEGQSRQYAELKSRIVADVKSLSLNANRIEALVEQLYDIN 330

Query: 304 NQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPS 362
            ++   E +++ +     G+ R  F++ +   E++ +WV+   K+    +     R    
Sbjct: 331 KRLISQEGRLMRLA-ESHGVARDEFLRHYQGQELDPHWVERVGKLGGKGWKNFTERGQDG 389

Query: 363 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD 422
           IK L++++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLVISIAKKYT+
Sbjct: 390 IKTLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTN 449

Query: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482
           RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM
Sbjct: 450 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 509

Query: 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542
           IETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+ED
Sbjct: 510 IETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEED 569

Query: 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEV 602
           SHLGDFIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEV
Sbjct: 570 SHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 629

Query: 603 GKQFDVTRERIRQIEAKALRKLR 625
           G+QF VTRERIRQIEAKALRKL+
Sbjct: 630 GQQFSVTRERIRQIEAKALRKLK 652


>gi|114778492|ref|ZP_01453336.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114551217|gb|EAU53776.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 660

 Score =  504 bits (1298), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 289/662 (43%), Positives = 409/662 (61%), Gaps = 63/662 (9%)

Query: 818  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 877
            +  NS+E++  +R+   ++ K GK+ G++T+ ++N  LP  ++  + +E +I  F  M +
Sbjct: 1    MSKNSQEQV-TIRELGSLMAK-GKQAGFITYDDLNKHLPGGLVSADRVEQLINVFTEMGV 58

Query: 878  SVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFG---RTKDPIKMYMREMGSVEL 934
                 V+D E           D     ++AL    S  G   R  DP++MY+REMG+VEL
Sbjct: 59   ----EVVDPERAPTGAYAMRKDRLRKEDSALRADTSQLGTVIRIDDPVRMYLREMGTVEL 114

Query: 935  LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI---------------SKNE 979
            LTR+GEIEIA+RIEEG   +  AI  CP+T  EI++  ++I                ++ 
Sbjct: 115  LTREGEIEIARRIEEGRMQVHEAICLCPSTFREIMLLGERIIQIRDEAMELGEEPSFRDI 174

Query: 980  IKIDE-IVDGLIDKNFSSNNRVIKGNKNNNE--------------EKILIESSSADLST- 1023
            I +DE +V+    K +   NR+ +  ++++E              E I   +++ D +  
Sbjct: 175  IDVDEKVVNSAAIKEY--ENRMSRSEEDDDEPVETEPKLDGEQLTEAIKARTATPDGTPM 232

Query: 1024 --------EQLEKLKYESLIKFSNIS-FH--FDKMRKAFEKEGYNSESYIKAHNNISN-- 1070
                    EQLE    E+L  F      H  F +++K   K   +    +++   +    
Sbjct: 233  QETVITKEEQLE----EALFHFGEAKKLHDDFIEVKKKLAKRPNDKALLLRSREVLDAML 288

Query: 1071 -EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 1129
             E++ I F+ + +++L    +N + +V + E+ I +  + +  MPR  F++ FP +E N 
Sbjct: 289  LELVSIPFSPRQLDQLVQRFKNAVEKVRRFERSIRDYAL-EARMPRKLFLETFPVDETNE 347

Query: 1130 NWVDNETKIQHDYNLILC--RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 1187
             W+D   K   D   +         IKE Q++L  ++ +  + + +L+D+ RK+  GE K
Sbjct: 348  RWIDELMKQNKDAAWVTAIEEVTGKIKENQRRLRRVEQETEMGVVELKDVARKLTMGEAK 407

Query: 1188 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247
             R+AKREM EANLRLVISIAKKYT+RGL FLDLIQEGNIGLMKAV+KFE+RRGYKFSTYA
Sbjct: 408  MRQAKREMIEANLRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFSTYA 467

Query: 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 1307
            TWWIRQAITRSIADQARTIRIPVHMIETINK+ R+SRQI QE G EP P  +A  +E+P 
Sbjct: 468  TWWIRQAITRSIADQARTIRIPVHMIETINKMMRVSRQIAQEIGREPTPEELAEHLELPV 527

Query: 1308 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 1367
            EK+ +I+++AKEPVS+E+P+GDDEDS LGDF+ED+N   P D+ + A++     ++L +L
Sbjct: 528  EKVLQILEVAKEPVSLETPIGDDEDSQLGDFVEDDNAENPLDSTIGAALAEATLEVLENL 587

Query: 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427
            T RE KVLRMRFGI M++DHTLEEVGKQF VTRERIRQIEAKALRKLRHPSR  KLK F 
Sbjct: 588  TDREQKVLRMRFGIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRKLRHPSRSQKLKTFA 647

Query: 1428 EG 1429
            + 
Sbjct: 648  DA 649



 Score =  487 bits (1253), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 281/648 (43%), Positives = 400/648 (61%), Gaps = 63/648 (9%)

Query: 28  IKSNSREEIENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDI 87
           +  NS+E++  +R+   ++ K GK+ G++T+ ++N  LP  ++  + +E +I  F  M +
Sbjct: 1   MSKNSQEQV-TIRELGSLMAK-GKQAGFITYDDLNKHLPGGLVSADRVEQLINVFTEMGV 58

Query: 88  SVSEHVLDTETLMLSNITSDDDVEEATEAALSTVDSDFG---RTKDPIKMYMREMGSVEL 144
                V+D E           D     ++AL    S  G   R  DP++MY+REMG+VEL
Sbjct: 59  ----EVVDPERAPTGAYAMRKDRLRKEDSALRADTSQLGTVIRIDDPVRMYLREMGTVEL 114

Query: 145 LTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKI---------------SKNE 189
           LTR+GEIEIA+RIEEG   +  AI  CP+T  EI++  ++I                ++ 
Sbjct: 115 LTREGEIEIARRIEEGRMQVHEAICLCPSTFREIMLLGERIIQIRDEAMELGEEPSFRDI 174

Query: 190 IKIDE-IVDGLIDKNFSSNNRVIKGNKNNNE--------------EKILIESSSADLST- 233
           I +DE +V+    K +   NR+ +  ++++E              E I   +++ D +  
Sbjct: 175 IDVDEKVVNSAAIKEY--ENRMSRSEEDDDEPVETEPKLDGEQLTEAIKARTATPDGTPM 232

Query: 234 --------EQLEKLKYESLIKFSNIS-FH--FDKMRKAFEKEGYNSESYIKAHNNISN-- 280
                   EQLE    E+L  F      H  F +++K   K   +    +++   +    
Sbjct: 233 QETVITKEEQLE----EALFHFGEAKKLHDDFIEVKKKLAKRPNDKALLLRSREVLDAML 288

Query: 281 -EMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINL 339
            E++ I F+ + +++L    +N + +V + E+ I +  + +  MPR  F++ FP +E N 
Sbjct: 289 LELVSIPFSPRQLDQLVQRFKNAVEKVRRFERSIRDYAL-EARMPRKLFLETFPVDETNE 347

Query: 340 NWVDNETKIQHDYNLILC--RNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMK 397
            W+D   K   D   +         IKE Q++L  ++ +  + + +L+D+ RK+  GE K
Sbjct: 348 RWIDELMKQNKDAAWVTAIEEVTGKIKENQRRLRRVEQETEMGVVELKDVARKLTMGEAK 407

Query: 398 ARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457
            R+AKREM EANLRLVISIAKKYT+RGL FLDLIQEGNIGLMKAV+KFE+RRGYKFSTYA
Sbjct: 408 MRQAKREMIEANLRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFSTYA 467

Query: 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPE 517
           TWWIRQAITRSIADQARTIRIPVHMIETINK+ R+SRQI QE G EP P  +A  +E+P 
Sbjct: 468 TWWIRQAITRSIADQARTIRIPVHMIETINKMMRVSRQIAQEIGREPTPEELAEHLELPV 527

Query: 518 EKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL 577
           EK+ +I+++AKEPVS+E+P+GDDEDS LGDF+ED+N   P D+ + A++     ++L +L
Sbjct: 528 EKVLQILEVAKEPVSLETPIGDDEDSQLGDFVEDDNAENPLDSTIGAALAEATLEVLENL 587

Query: 578 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           T RE KVLRMRFGI M++DHTLEEVGKQF VTRERIRQIEAKALRKLR
Sbjct: 588 TDREQKVLRMRFGIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRKLR 635


>gi|329114160|ref|ZP_08242922.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
 gi|326696236|gb|EGE47915.1| RNA polymerase sigma factor RpoD [Acetobacter pomorum DM001]
          Length = 672

 Score =  504 bits (1297), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 289/649 (44%), Positives = 389/649 (59%), Gaps = 70/649 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 38   KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 86

Query: 894  ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 929
               D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 87   --EDNDNEEAEPKKAAAESEDADAEEEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 144

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 145  GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 202

Query: 990  IDKNFSSNNRVIKGNKNNNEEKIL-----------------IESSSADLSTEQLE-KLKY 1031
            ++   S  N + +G      E                    IES  + LS   LE KLK 
Sbjct: 203  LEAMQSGGNPLEEGGDGTFNEAESDSDSEEAEEPETEGEGDIESEGSGLSLSALEEKLKP 262

Query: 1032 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
            E L  F  I   +  +RK             + +G   E+Y+     +  ++  +     
Sbjct: 263  EILAHFDEIEPLYAALRKLQVQRIEALTSGEDVDGNFEENYVALREKLVGKVEQVHLHNN 322

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 1139
             IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 323  RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSALSG 381

Query: 1140 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 1199
              +   + ++  ++ +L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 382  RSWKNFVAKHANTVVDLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 441

Query: 1200 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 1259
            LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 442  LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 501

Query: 1260 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 1319
            ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 502  ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 561

Query: 1320 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 1379
            P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 562  PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 621

Query: 1380 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 622  GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 670



 Score =  486 bits (1252), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 281/636 (44%), Positives = 379/636 (59%), Gaps = 70/636 (11%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 38  KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 86

Query: 104 ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 139
              D+D EEA                        E+    V+++  GRT DP++MY+REM
Sbjct: 87  --EDNDNEEAEPKKAAAESEDADAEEEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 144

Query: 140 GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 199
           G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 145 GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 202

Query: 200 IDKNFSSNNRVIKGNKNNNEEKIL-----------------IESSSADLSTEQLE-KLKY 241
           ++   S  N + +G      E                    IES  + LS   LE KLK 
Sbjct: 203 LEAMQSGGNPLEEGGDGTFNEAESDSDSEEAEEPETEGEGDIESEGSGLSLSALEEKLKP 262

Query: 242 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
           E L  F  I   +  +RK             + +G   E+Y+     +  ++  +     
Sbjct: 263 EILAHFDEIEPLYAALRKLQVQRIEALTSGEDVDGNFEENYVALREKLVGKVEQVHLHNN 322

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 349
            IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 323 RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSALSG 381

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             +   + ++  ++ +L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 382 RSWKNFVAKHANTVVDLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 441

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 442 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 501

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 502 ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 561

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 562 PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 621

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 622 GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 657


>gi|296284010|ref|ZP_06862008.1| RNA polymerase sigma factor RpoD [Citromicrobium bathyomarinum JL354]
          Length = 667

 Score =  504 bits (1297), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 290/653 (44%), Positives = 398/653 (60%), Gaps = 66/653 (10%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 890
             K LI   K+RGY+T+ E+N+ LP+  +  + IE I      M + +  S+  +++E   
Sbjct: 23   IKKLISKAKKRGYVTYDELNEALPQGEMSSDQIEDIQAAISEMGVQIVESDDEVESEKDE 82

Query: 891  LSNITSDD----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
            +  I  D     D + A  A   TVD+   RT DP++MY+REMG+VELL+R+GEI IAKR
Sbjct: 83   VEEIAPDSGAKKDTKSAAAAPKKTVDA---RTDDPVRMYLREMGAVELLSREGEIAIAKR 139

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE G   MI  +   P T   I+  +D +++ E+++ EI+D  +D   S    V K  + 
Sbjct: 140  IEAGRDTMIIGLCESPITFHAIIQWSDALNEGEMQLREILD--LDAMLSKEPPVDKMEEE 197

Query: 1007 NNEEKILIESSSAD-------------------------------------LSTEQLEK- 1028
            N ++   I   +A                                      +S  Q+E  
Sbjct: 198  NEDDSGEISEETAGPTIREDDDDDDDETAEGDEDGDGESKRRDDDDEEDNTMSLAQMEAA 257

Query: 1029 LKYESLIKFSNISFHFDKMRK-------------AFEKEGYNSESYIKAHNNISNEMLGI 1075
            LK ++L +F+ I+  F K  K             AF       + Y      ++ E+  +
Sbjct: 258  LKPDALERFARITDLFKKFEKLQAERVDVLGRGDAFP--AAKEKKYEDLREQLTAEVESV 315

Query: 1076 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 1135
            +F A  IE L D L     ++T +  Q+L +   +  + R+ F+  +  NE++  W+ + 
Sbjct: 316  QFHATKIEFLVDNLYAFNRRLTALGGQMLRLA-ERHKIKRIDFLDAYLGNEMDDEWLTSR 374

Query: 1136 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 1195
            TK    +     +   SI+ ++ ++ ++ +   + L + R I   +  GE +AR AK+EM
Sbjct: 375  TK-DKKWAAFAEKEAESIERIRTEISDIASQTGMALEEFRRIVNMVQKGEREARIAKKEM 433

Query: 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255
             EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 434  VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 493

Query: 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315
            TRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+RK+MK
Sbjct: 494  TRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMK 553

Query: 1316 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 1375
            IAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ ++++  V  +L SLTPRE +VL
Sbjct: 554  IAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQSNLKETVTRVLASLTPREERVL 613

Query: 1376 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            RMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 614  RMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 666



 Score =  487 bits (1254), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 283/640 (44%), Positives = 388/640 (60%), Gaps = 66/640 (10%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 100
            K LI   K+RGY+T+ E+N+ LP+  +  + IE I      M + +  S+  +++E   
Sbjct: 23  IKKLISKAKKRGYVTYDELNEALPQGEMSSDQIEDIQAAISEMGVQIVESDDEVESEKDE 82

Query: 101 LSNITSDD----DVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
           +  I  D     D + A  A   TVD+   RT DP++MY+REMG+VELL+R+GEI IAKR
Sbjct: 83  VEEIAPDSGAKKDTKSAAAAPKKTVDA---RTDDPVRMYLREMGAVELLSREGEIAIAKR 139

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE G   MI  +   P T   I+  +D +++ E+++ EI+D  +D   S    V K  + 
Sbjct: 140 IEAGRDTMIIGLCESPITFHAIIQWSDALNEGEMQLREILD--LDAMLSKEPPVDKMEEE 197

Query: 217 NNEEKILIESSSAD-------------------------------------LSTEQLEK- 238
           N ++   I   +A                                      +S  Q+E  
Sbjct: 198 NEDDSGEISEETAGPTIREDDDDDDDETAEGDEDGDGESKRRDDDDEEDNTMSLAQMEAA 257

Query: 239 LKYESLIKFSNISFHFDKMRK-------------AFEKEGYNSESYIKAHNNISNEMLGI 285
           LK ++L +F+ I+  F K  K             AF       + Y      ++ E+  +
Sbjct: 258 LKPDALERFARITDLFKKFEKLQAERVDVLGRGDAFP--AAKEKKYEDLREQLTAEVESV 315

Query: 286 RFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNE 345
           +F A  IE L D L     ++T +  Q+L +   +  + R+ F+  +  NE++  W+ + 
Sbjct: 316 QFHATKIEFLVDNLYAFNRRLTALGGQMLRLA-ERHKIKRIDFLDAYLGNEMDDEWLTSR 374

Query: 346 TKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREM 405
           TK    +     +   SI+ ++ ++ ++ +   + L + R I   +  GE +AR AK+EM
Sbjct: 375 TK-DKKWAAFAEKEAESIERIRTEISDIASQTGMALEEFRRIVNMVQKGEREARIAKKEM 433

Query: 406 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465
            EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI
Sbjct: 434 VEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 493

Query: 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525
           TRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+RK+MK
Sbjct: 494 TRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVRKVMK 553

Query: 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVL 585
           IAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ ++++  V  +L SLTPRE +VL
Sbjct: 554 IAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQSNLKETVTRVLASLTPREERVL 613

Query: 586 RMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           RMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 614 RMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|197106036|ref|YP_002131413.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
 gi|196479456|gb|ACG78984.1| RNA polymerase sigma factor RpoD [Phenylobacterium zucineum HLK1]
          Length = 638

 Score =  503 bits (1296), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 280/624 (44%), Positives = 384/624 (61%), Gaps = 41/624 (6%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            KKF   IK  K RGY+T  E+N  +P + +  E IE  +     M ++V E   D E   
Sbjct: 29   KKF---IKQAKARGYVTMDELNKVMPSEEVTSEAIEDTLAMLNEMGVNVVESEEDAEGGE 85

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
            ++       V E +    +T +  + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 86   VA-------VREESAVVETTKEPAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 138

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
               MI  +     T   I++  +++    I + E++D  +++ +   N+     +    E
Sbjct: 139  RDTMIRGLCESALTFEAIMVWREELEGGRILLREVID--LEQTYGGQNQGEAPAEAAEAE 196

Query: 1011 KILI--------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK--- 1053
            +                 + +   +S  + E L+   +     I+  F+  R   EK   
Sbjct: 197  EPEAEGAEGEGESDDDFDDGAGPTISAMEAE-LREGVMATLDAIAAEFESFRLLQEKLVA 255

Query: 1054 ---------EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 1104
                     EG + ++Y  A   I   +  ++     IE L + L     ++  +E ++L
Sbjct: 256  AKLKGEDLSEG-DRKAYQAATGAIVQHLKTLKLNNNRIEALVEQLYAINKRLMVLEGRLL 314

Query: 1105 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164
             +  +  G+ R  F+K +  NE+  +W D    +   +      +   I E++ ++  L 
Sbjct: 315  RLA-DSYGISRQEFLKAYFGNEMRPDWTDMVKPLGVRWTKFAENDASQIGEIRNEIAALA 373

Query: 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 1224
             +  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 374  QETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 433

Query: 1225 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 1284
            NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI R SR
Sbjct: 434  NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 493

Query: 1285 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 1344
            Q+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+N 
Sbjct: 494  QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 553

Query: 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404
            + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIR
Sbjct: 554  VLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 613

Query: 1405 QIEAKALRKLRHPSRYYKLKIFLE 1428
            QIEAKALRKL+HPSR  KL+ FL+
Sbjct: 614  QIEAKALRKLKHPSRSRKLRSFLD 637



 Score =  486 bits (1251), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 272/611 (44%), Positives = 374/611 (61%), Gaps = 41/611 (6%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           KKF   IK  K RGY+T  E+N  +P + +  E IE  +     M ++V E   D E   
Sbjct: 29  KKF---IKQAKARGYVTMDELNKVMPSEEVTSEAIEDTLAMLNEMGVNVVESEEDAEGGE 85

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
           ++       V E +    +T +  + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 86  VA-------VREESAVVETTKEPAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 138

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
              MI  +     T   I++  +++    I + E++D  +++ +   N+     +    E
Sbjct: 139 RDTMIRGLCESALTFEAIMVWREELEGGRILLREVID--LEQTYGGQNQGEAPAEAAEAE 196

Query: 221 KILI--------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEK--- 263
           +                 + +   +S  + E L+   +     I+  F+  R   EK   
Sbjct: 197 EPEAEGAEGEGESDDDFDDGAGPTISAMEAE-LREGVMATLDAIAAEFESFRLLQEKLVA 255

Query: 264 ---------EGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQIL 314
                    EG + ++Y  A   I   +  ++     IE L + L     ++  +E ++L
Sbjct: 256 AKLKGEDLSEG-DRKAYQAATGAIVQHLKTLKLNNNRIEALVEQLYAINKRLMVLEGRLL 314

Query: 315 EIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374
            +  +  G+ R  F+K +  NE+  +W D    +   +      +   I E++ ++  L 
Sbjct: 315 RLA-DSYGISRQEFLKAYFGNEMRPDWTDMVKPLGVRWTKFAENDASQIGEIRNEIAALA 373

Query: 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEG 434
            +  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEG
Sbjct: 374 QETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 433

Query: 435 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISR 494
           NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKI R SR
Sbjct: 434 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSR 493

Query: 495 QILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENM 554
           Q+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+N 
Sbjct: 494 QMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNA 553

Query: 555 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614
           + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIR
Sbjct: 554 VLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 613

Query: 615 QIEAKALRKLR 625
           QIEAKALRKL+
Sbjct: 614 QIEAKALRKLK 624


>gi|118591038|ref|ZP_01548438.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118436560|gb|EAV43201.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 662

 Score =  503 bits (1295), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 288/637 (45%), Positives = 394/637 (61%), Gaps = 47/637 (7%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IK  K+RGY+T+ E+N+ LP + +  E IE  +     M I+V +   D       
Sbjct: 31   VKKMIKAAKKRGYVTYDELNEVLPSEQVSSEKIEDTMSMLSDMGINVIDS--DEAEEGPE 88

Query: 893  NITSDDDVEEATEA-ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
             +   D V  +T A A ST      RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 89   EVDGGDLVAASTTALAKSTTKEPADRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 148

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SNNRVI 1001
            + MI  +   P T   I+I  D++++ ++ + +I+D  ++  ++          +N+ V 
Sbjct: 149  EAMIAGLCESPLTFQAIIIWRDELNEAQVLLRDIID--LEATYAGPDAKAGPAVANDDVA 206

Query: 1002 KGNKNNNEEKILIES------------------SSADLSTEQLEKLKYESLIKFSNISFH 1043
             G  N+       E                   S+  LS  + E LK   L  F NI+ +
Sbjct: 207  PGEGNSENSGGASEDTESEDGEGDGDDDDDEFESNVSLSAMEAE-LKPGVLETFDNIADN 265

Query: 1044 FDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 1092
            + K+R+  ++   N              Y K   +I  ++  +      I+ L   L + 
Sbjct: 266  YKKLRRLQDQLVENKLANKTLSPSQERRYKKLKEDIIVDVKSLSLNQNRIDALVAQLYDI 325

Query: 1093 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIP 1151
              ++   E ++L +  +   + R  F+K +   E++ NW+     +    +   + +   
Sbjct: 326  NKRLMGYEGRLLRL-ADSYNVDRTDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKE 384

Query: 1152 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 1211
            +++EL+Q +  L T+  L + + R I   +  GE +AR AK+EM EANLRLVISIAKKYT
Sbjct: 385  TVRELRQDIQTLATETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYT 444

Query: 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271
            +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 445  NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 504

Query: 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331
            MIETINKI R SRQ+L E G EP P  +A K++MP EK+RK++KIAKEP+S+E+P+GD+E
Sbjct: 505  MIETINKIVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEE 564

Query: 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 1391
            DSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEE
Sbjct: 565  DSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 624

Query: 1392 VGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 625  VGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 661



 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 280/624 (44%), Positives = 384/624 (61%), Gaps = 47/624 (7%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IK  K+RGY+T+ E+N+ LP + +  E IE  +     M I+V +   D       
Sbjct: 31  VKKMIKAAKKRGYVTYDELNEVLPSEQVSSEKIEDTMSMLSDMGINVIDS--DEAEEGPE 88

Query: 103 NITSDDDVEEATEA-ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
            +   D V  +T A A ST      RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 89  EVDGGDLVAASTTALAKSTTKEPADRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 148

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------SNNRVI 211
           + MI  +   P T   I+I  D++++ ++ + +I+D  ++  ++          +N+ V 
Sbjct: 149 EAMIAGLCESPLTFQAIIIWRDELNEAQVLLRDIID--LEATYAGPDAKAGPAVANDDVA 206

Query: 212 KGNKNNNEEKILIES------------------SSADLSTEQLEKLKYESLIKFSNISFH 253
            G  N+       E                   S+  LS  + E LK   L  F NI+ +
Sbjct: 207 PGEGNSENSGGASEDTESEDGEGDGDDDDDEFESNVSLSAMEAE-LKPGVLETFDNIADN 265

Query: 254 FDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQ 302
           + K+R+  ++   N              Y K   +I  ++  +      I+ L   L + 
Sbjct: 266 YKKLRRLQDQLVENKLANKTLSPSQERRYKKLKEDIIVDVKSLSLNQNRIDALVAQLYDI 325

Query: 303 INQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIP 361
             ++   E ++L +  +   + R  F+K +   E++ NW+     +    +   + +   
Sbjct: 326 NKRLMGYEGRLLRL-ADSYNVDRTDFLKQYQGAELDPNWLRKVANLSTRGWKNFIAKEKE 384

Query: 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT 421
           +++EL+Q +  L T+  L + + R I   +  GE +AR AK+EM EANLRLVISIAKKYT
Sbjct: 385 TVRELRQDIQTLATETGLEITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYT 444

Query: 422 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481
           +RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH
Sbjct: 445 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 504

Query: 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541
           MIETINKI R SRQ+L E G EP P  +A K++MP EK+RK++KIAKEP+S+E+P+GD+E
Sbjct: 505 MIETINKIVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPIGDEE 564

Query: 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEE 601
           DSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEE
Sbjct: 565 DSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE 624

Query: 602 VGKQFDVTRERIRQIEAKALRKLR 625
           VG+QF VTRERIRQIEAKALRKL+
Sbjct: 625 VGQQFSVTRERIRQIEAKALRKLK 648


>gi|421851555|ref|ZP_16284248.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus subsp. pasteurianus LMG 1262 = NBRC 106471]
 gi|371480058|dbj|GAB29451.1| DNA-directed RNA polymerase sigma factor RpoD [Acetobacter
            pasteurianus subsp. pasteurianus LMG 1262 = NBRC 106471]
          Length = 663

 Score =  503 bits (1295), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 289/649 (44%), Positives = 389/649 (59%), Gaps = 70/649 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 29   KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 77

Query: 894  ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 929
               D+D EE                         E+    V+++  GRT DP++MY+REM
Sbjct: 78   --EDNDNEETEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 135

Query: 930  GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 989
            G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 136  GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 193

Query: 990  IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 1031
            ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 194  LEAMQSGGNPLEEGGDGTFNEAESDSEAEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 253

Query: 1032 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 1080
            E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 254  EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 313

Query: 1081 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 1139
             IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 314  RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 372

Query: 1140 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 1199
              +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 373  RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 432

Query: 1200 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 1259
            LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 433  LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 492

Query: 1260 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 1319
            ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 493  ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 552

Query: 1320 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 1379
            P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 553  PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 612

Query: 1380 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 613  GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 661



 Score =  486 bits (1250), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 281/636 (44%), Positives = 379/636 (59%), Gaps = 70/636 (11%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  G+ERG +TF E+N  LP+D +  E IE I+     M I V E+           
Sbjct: 29  KKLIAKGRERGCITFDELNAVLPQDKMSSEQIEDIMAVLSEMGIQVVEN----------- 77

Query: 104 ITSDDDVEEA-----------------------TEAALSTVDSD-FGRTKDPIKMYMREM 139
              D+D EE                         E+    V+++  GRT DP++MY+REM
Sbjct: 78  --EDNDNEETEPKKAAAESDDAEEEAEAETEAEAESPTGNVNAESVGRTDDPVRMYLREM 135

Query: 140 GSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGL 199
           G+VELL+R+GEI IAKRIE G  +MI  +   P T   I+   + I  NE+ + +IVD  
Sbjct: 136 GTVELLSREGEIAIAKRIEAGRDEMIGGLCESPLTFRAIISWHEMIRNNEMLLRDIVD-- 193

Query: 200 IDKNFSSNNRVIKGNKNN-----------------NEEKILIESSSADLSTEQLE-KLKY 241
           ++   S  N + +G                      E +  IES  + LS   LE KLK 
Sbjct: 194 LEAMQSGGNPLEEGGDGTFNEAESDSEAEEAEEPEAEGEGDIESEGSGLSLSALEEKLKP 253

Query: 242 ESLIKFSNISFHFDKMRK-----------AFEKEGYNSESYIKAHNNISNEMLGIRFTAK 290
           E L  F  I   + ++RK             + +G   ESY+     +  ++  +     
Sbjct: 254 EILAHFDEIEPLYAELRKLQVQRIEALTSGEDVDGNFEESYVALREKLVGKVEQVHLHNN 313

Query: 291 SIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ- 349
            IE L   L+    ++  +E ++L +    C + R  F+  +   E++  W+D  + +  
Sbjct: 314 RIEDLVAQLKQMFQKLNMLEGRMLRLA-ESCRVSREDFLLKYRGRELDPGWMDMVSGLSG 372

Query: 350 HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEAN 409
             +   + ++  ++  L+ ++  L  +  LP+ + R +   +  GE  + +AK+EM EAN
Sbjct: 373 RSWKNFVAKHANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARGERDSARAKKEMIEAN 432

Query: 410 LRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 469
           LRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI
Sbjct: 433 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 492

Query: 470 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE 529
           ADQARTIRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKE
Sbjct: 493 ADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKE 552

Query: 530 PVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRF 589
           P+S+E+P+GD+EDSHLGDFIED+  + P DAA+  ++R     +L SLTPRE +VLRMRF
Sbjct: 553 PISLETPIGDEEDSHLGDFIEDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRF 612

Query: 590 GIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           GI M++DHTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 613 GIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 648


>gi|347760218|ref|YP_004867779.1| DNA-directed RNA polymerase sigma 70 [Gluconacetobacter xylinus NBRC
            3288]
 gi|347579188|dbj|BAK83409.1| DNA-directed RNA polymerase sigma 70 [Gluconacetobacter xylinus NBRC
            3288]
          Length = 659

 Score =  503 bits (1294), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 293/630 (46%), Positives = 393/630 (62%), Gaps = 38/630 (6%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 891
            K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    DTET   
Sbjct: 31   KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDDTETPAA 90

Query: 892  SNITSDDDVEEATE---AALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 947
                +DD  EE TE    A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91   PEGKADDTAEEETESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 948  EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 1007
            E G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S  N   +  +  
Sbjct: 151  EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGNDPAEAAEGE 208

Query: 1008 N----------------EEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK- 1049
            +                E +   E   A LS   LE KLK E L +F  +   +  + + 
Sbjct: 209  DAFAENEGTENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYQALHRV 268

Query: 1050 -AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQI 1099
             A   E + + S I A      E L +    K          IE L + L+    ++  +
Sbjct: 269  QAERLEKFTAGSDISAEEESRYEHLRLELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGL 328

Query: 1100 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQ 1158
            E ++L +      + R  F+  +   E++  W+D    +    +   + ++  ++  L+ 
Sbjct: 329  EGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVIRLRN 387

Query: 1159 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 1218
            ++ +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 388  QVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFL 447

Query: 1219 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 1278
            DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 448  DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 507

Query: 1279 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338
            + R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 508  LVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 567

Query: 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 1398
            IED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+V
Sbjct: 568  IEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNV 627

Query: 1399 TRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            TRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 628  TRERIRQIEAKALRKLKHPSRSRKLRSFLD 657



 Score =  485 bits (1249), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 285/617 (46%), Positives = 383/617 (62%), Gaps = 38/617 (6%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVL--DTETLML 101
           K LI  GKERGY+TF E+N  LP+D +  E IE ++     M + V E+    DTET   
Sbjct: 31  KKLIARGKERGYITFDELNAVLPQDQMSSEQIEDVMAALSEMGMQVVENEDNDDTETPAA 90

Query: 102 SNITSDDDVEEATE---AALSTVDSD-FGRTKDPIKMYMREMGSVELLTRDGEIEIAKRI 157
               +DD  EE TE    A   VD++  GRT DP++MY+REMGSVELL+R+GEI IAKRI
Sbjct: 91  PEGKADDTAEEETESEEPAAGNVDTESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRI 150

Query: 158 EEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNN 217
           E G  +MI  +   P T   I+   +++   E+ + +IVD  ++   S  N   +  +  
Sbjct: 151 EAGRDEMIGGLCESPLTFRAIISWHERLKAGEMLLRDIVD--LEAMQSGGNDPAEAAEGE 208

Query: 218 N----------------EEKILIESSSADLSTEQLE-KLKYESLIKFSNISFHFDKMRK- 259
           +                E +   E   A LS   LE KLK E L +F  +   +  + + 
Sbjct: 209 DAFAENEGTENEEAEETEGEGEGEGEGAGLSLSALEEKLKPEILEQFEEVEALYQALHRV 268

Query: 260 -AFEKEGYNSESYIKAHNNISNEMLGIRFTAK---------SIEKLCDTLRNQINQVTQI 309
            A   E + + S I A      E L +    K          IE L + L+    ++  +
Sbjct: 269 QAERLEKFTAGSDISAEEESRYEHLRLELVGKVQQVHLHNARIEVLVEHLKEIFQRLNGL 328

Query: 310 EKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQ 368
           E ++L +      + R  F+  +   E++  W+D    +    +   + ++  ++  L+ 
Sbjct: 329 EGRMLRLA-ESTRVSRDDFLLKYRGRELDPGWMDMAAALPGKSWKNFIAKHGETVIRLRN 387

Query: 369 KLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428
           ++ +L  +  LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFL
Sbjct: 388 QVADLTQETGLPVGEFRRVYATVSRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQFL 447

Query: 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 488
           DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK
Sbjct: 448 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 507

Query: 489 ISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548
           + R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDF
Sbjct: 508 LVRTSRQMLHEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDF 567

Query: 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDV 608
           IED+  + P DAA+  ++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+V
Sbjct: 568 IEDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNV 627

Query: 609 TRERIRQIEAKALRKLR 625
           TRERIRQIEAKALRKL+
Sbjct: 628 TRERIRQIEAKALRKLK 644


>gi|154252764|ref|YP_001413588.1| RNA polymerase sigma factor RpoD [Parvibaculum lavamentivorans DS-1]
 gi|154156714|gb|ABS63931.1| RNA polymerase, sigma 70 subunit, RpoD [Parvibaculum lavamentivorans
            DS-1]
          Length = 656

 Score =  502 bits (1293), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 290/643 (45%), Positives = 399/643 (62%), Gaps = 67/643 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K +IK  K RG++T+ E+N  LP +    E IE  +     M I+V E           N
Sbjct: 32   KKMIKAAKARGFVTYDELNKVLPSEEFSSEQIEDTLSMLSEMGINVVE-----------N 80

Query: 894  ITSDDDVEEA-----------------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 936
              ++D+ E A                   A  +T  S   RT DP++MY+REMGSVELL+
Sbjct: 81   DEAEDNAEGADGEADEDRDDEEAPTGKAVATTTTTSSSLDRTDDPVRMYLREMGSVELLS 140

Query: 937  RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 996
            R+GEI IAKRIE G + MI  +   P T   I+I  D++++ +I + +I+D  +D  F+ 
Sbjct: 141  REGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNEGKILLRDIID--LDATFAG 198

Query: 997  NNRVIKGNKNNNEEKILI-------------------ESSSADLSTEQLEKLKYESLIKF 1037
             +      K ++ +  L                    + +S  L+  + E LK + L  F
Sbjct: 199  PD----AKKVDHSQAALAGEAPPRIEPEEEEVDEDGEDDNSMSLAAMEAE-LKPKVLETF 253

Query: 1038 SNISFHFDKMRK--------AFEKEGYNS---ESYIKAHNNISNEMLGIRFTAKSIEKLC 1086
              I+  + K+RK        A + E  +S   + Y K  +++  E+  +      IE L 
Sbjct: 254  DTIAADYKKLRKLQDQKVELALQGEALSSAQEKKYQKLTSDLIEEVKSLSLNNNRIESLV 313

Query: 1087 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 1146
            + L     ++  +E ++L +     G+PR  F+K +  NE++ NW+   ++++    +  
Sbjct: 314  EQLYAINKRLMGLEGRLLRLA-ESHGIPRDEFLKQYFGNELDPNWIRRVSRLKGKGWVNF 372

Query: 1147 CRN-IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
             ++    +K+L+Q++  L ++  L + + R I   +  GE +AR AK+EM EANLRLVIS
Sbjct: 373  TKDERDQVKDLRQEIQTLASETGLDIQEYRRIVSGVQKGEREARIAKKEMVEANLRLVIS 432

Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
            IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 433  IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 492

Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 1325
            IRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+
Sbjct: 493  IRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLET 552

Query: 1326 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 1385
            P+GD+EDSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++
Sbjct: 553  PIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 612

Query: 1386 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 613  DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 655



 Score =  485 bits (1248), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 282/630 (44%), Positives = 389/630 (61%), Gaps = 67/630 (10%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K +IK  K RG++T+ E+N  LP +    E IE  +     M I+V E           N
Sbjct: 32  KKMIKAAKARGFVTYDELNKVLPSEEFSSEQIEDTLSMLSEMGINVVE-----------N 80

Query: 104 ITSDDDVEEA-----------------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLT 146
             ++D+ E A                   A  +T  S   RT DP++MY+REMGSVELL+
Sbjct: 81  DEAEDNAEGADGEADEDRDDEEAPTGKAVATTTTTSSSLDRTDDPVRMYLREMGSVELLS 140

Query: 147 RDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS 206
           R+GEI IAKRIE G + MI  +   P T   I+I  D++++ +I + +I+D  +D  F+ 
Sbjct: 141 REGEIAIAKRIEAGRETMIAGLCESPLTFQAIIIWRDELNEGKILLRDIID--LDATFAG 198

Query: 207 NNRVIKGNKNNNEEKILI-------------------ESSSADLSTEQLEKLKYESLIKF 247
            +      K ++ +  L                    + +S  L+  + E LK + L  F
Sbjct: 199 PD----AKKVDHSQAALAGEAPPRIEPEEEEVDEDGEDDNSMSLAAMEAE-LKPKVLETF 253

Query: 248 SNISFHFDKMRK--------AFEKEGYNS---ESYIKAHNNISNEMLGIRFTAKSIEKLC 296
             I+  + K+RK        A + E  +S   + Y K  +++  E+  +      IE L 
Sbjct: 254 DTIAADYKKLRKLQDQKVELALQGEALSSAQEKKYQKLTSDLIEEVKSLSLNNNRIESLV 313

Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 356
           + L     ++  +E ++L +     G+PR  F+K +  NE++ NW+   ++++    +  
Sbjct: 314 EQLYAINKRLMGLEGRLLRLA-ESHGIPRDEFLKQYFGNELDPNWIRRVSRLKGKGWVNF 372

Query: 357 CRN-IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
            ++    +K+L+Q++  L ++  L + + R I   +  GE +AR AK+EM EANLRLVIS
Sbjct: 373 TKDERDQVKDLRQEIQTLASETGLDIQEYRRIVSGVQKGEREARIAKKEMVEANLRLVIS 432

Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
           IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 433 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 492

Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535
           IRIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+
Sbjct: 493 IRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLET 552

Query: 536 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 595
           P+GD+EDSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++
Sbjct: 553 PIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 612

Query: 596 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 613 DHTLEEVGQQFSVTRERIRQIEAKALRKLK 642


>gi|347528800|ref|YP_004835547.1| RNA polymerase sigma factor RpoD [Sphingobium sp. SYK-6]
 gi|345137481|dbj|BAK67090.1| RNA polymerase sigma factor RpoD [Sphingobium sp. SYK-6]
          Length = 678

 Score =  502 bits (1292), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 285/669 (42%), Positives = 396/669 (59%), Gaps = 92/669 (13%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LI   K+RGY+T+ E+N+ LP+D +  E IE ++     M +++ E           
Sbjct: 28   IKKLIARAKKRGYITYDELNNALPQDQMSSEQIEDVMSALNDMGVNIVE----------- 76

Query: 893  NITSDDDVEEATEAALSTVDS-----------------DFGRTKDPIKMYMREMGSVELL 935
            N    DD E+  E    T+D                     RT DP++MY+REMG+VELL
Sbjct: 77   NDEQGDDSEDGAEPEADTIDGAAEDEDGSGNVGEKKKETVDRTDDPVRMYLREMGAVELL 136

Query: 936  TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--DGLIDKN 993
            +R+GEI IAKRIE G   MI  +   PTT   I+  ++ ++  E+++ EI+  D ++ K+
Sbjct: 137  SREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEWSNALNNGEMQLREILDLDAMLSKD 196

Query: 994  FSSNN-------------------------------------------RVIKGNKNNNEE 1010
             +  +                                           R  +  + + E+
Sbjct: 197  PAPESLSEDGEGDDDGEISEKTAGPSFKEEEDVEEESADDDEESMVERRTPRAEEEDEED 256

Query: 1011 KILIESSSADLSTEQLEKLKYESLIKFSNIS---FHFDKMRKA--------FEKEGYNSE 1059
              L  ++  +L       LK  +L KF+NI+     F K+++A         E    +  
Sbjct: 257  NTLSLAAMEEL-------LKPAALEKFANITQLYSAFGKIQQARLIALGNGVEFPAKDEA 309

Query: 1060 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 1119
            SY K   +++ E+  ++F  + IE L D L     ++T +  Q+L +   +  +PR  F+
Sbjct: 310  SYHKLREDLTAEVESVQFHQQKIEYLVDQLYAFNRRLTTLGGQMLRLA-ERHKVPRKDFL 368

Query: 1120 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 1179
              +  +E++  W++   KI   ++        +++ ++ ++  +       L + R I  
Sbjct: 369  DQYVGHELDEAWLEKVGKIDKKWSAFASAEAGAVERIRSEVAEIAQASGTSLPEFRRIVN 428

Query: 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 1239
             +  GE +AR AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 429  MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 488

Query: 1240 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 1299
            GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +
Sbjct: 489  GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEM 548

Query: 1300 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 1359
            A ++ MP EK+RK+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  
Sbjct: 549  AERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKET 608

Query: 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419
            V  +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR
Sbjct: 609  VTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 668

Query: 1420 YYKLKIFLE 1428
              K++ FL+
Sbjct: 669  SRKMRSFLD 677



 Score =  485 bits (1249), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 278/656 (42%), Positives = 386/656 (58%), Gaps = 92/656 (14%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K LI   K+RGY+T+ E+N+ LP+D +  E IE ++     M +++ E           
Sbjct: 28  IKKLIARAKKRGYITYDELNNALPQDQMSSEQIEDVMSALNDMGVNIVE----------- 76

Query: 103 NITSDDDVEEATEAALSTVDS-----------------DFGRTKDPIKMYMREMGSVELL 145
           N    DD E+  E    T+D                     RT DP++MY+REMG+VELL
Sbjct: 77  NDEQGDDSEDGAEPEADTIDGAAEDEDGSGNVGEKKKETVDRTDDPVRMYLREMGAVELL 136

Query: 146 TRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV--DGLIDKN 203
           +R+GEI IAKRIE G   MI  +   PTT   I+  ++ ++  E+++ EI+  D ++ K+
Sbjct: 137 SREGEIAIAKRIEAGRDTMILGLCESPTTFNAIIEWSNALNNGEMQLREILDLDAMLSKD 196

Query: 204 FSSNN-------------------------------------------RVIKGNKNNNEE 220
            +  +                                           R  +  + + E+
Sbjct: 197 PAPESLSEDGEGDDDGEISEKTAGPSFKEEEDVEEESADDDEESMVERRTPRAEEEDEED 256

Query: 221 KILIESSSADLSTEQLEKLKYESLIKFSNIS---FHFDKMRKA--------FEKEGYNSE 269
             L  ++  +L       LK  +L KF+NI+     F K+++A         E    +  
Sbjct: 257 NTLSLAAMEEL-------LKPAALEKFANITQLYSAFGKIQQARLIALGNGVEFPAKDEA 309

Query: 270 SYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFI 329
           SY K   +++ E+  ++F  + IE L D L     ++T +  Q+L +   +  +PR  F+
Sbjct: 310 SYHKLREDLTAEVESVQFHQQKIEYLVDQLYAFNRRLTTLGGQMLRLA-ERHKVPRKDFL 368

Query: 330 KVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINR 389
             +  +E++  W++   KI   ++        +++ ++ ++  +       L + R I  
Sbjct: 369 DQYVGHELDEAWLEKVGKIDKKWSAFASAEAGAVERIRSEVAEIAQASGTSLPEFRRIVN 428

Query: 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRR 449
            +  GE +AR AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRR
Sbjct: 429 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 488

Query: 450 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVI 509
           GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +
Sbjct: 489 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEM 548

Query: 510 AIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSV 569
           A ++ MP EK+RK+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  
Sbjct: 549 AERLSMPLEKVRKVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKET 608

Query: 570 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           V  +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 609 VTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 664


>gi|410943501|ref|ZP_11375242.1| RNA polymerase sigma factor RpoD [Gluconobacter frateurii NBRC
            101659]
          Length = 649

 Score =  502 bits (1292), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 283/621 (45%), Positives = 388/621 (62%), Gaps = 28/621 (4%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K LI  G+ERG++TF E+N  LP+D +  E IE ++     M I V E+    E     
Sbjct: 30   VKRLIAKGRERGHITFDELNAVLPQDQMSSEQIEDVMAALSEMGIQVLENEEQDEPETAQ 89

Query: 893  NITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 951
            +  + ++ EE+ E     +D++   RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 90   D-EAKEEAEESDEPQGGNIDAEAASRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 148

Query: 952  KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 1011
             +MI  +   P TI  I+   +++   E+ + +IVD    ++        +G + +    
Sbjct: 149  DEMIGGLCESPLTIRAIISWHERLKDGEMLLRDIVDLEASQSGGPGPEDEEGEEGDEPAD 208

Query: 1012 ILI------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR----KAFEKEG 1055
                           E S   LS  + EKLK E L +F  I   + K+R    K  E   
Sbjct: 209  DDSDDDAEDGDGEQQEGSGLSLSALE-EKLKPEILARFEAIEPLYHKLRQLQTKRLEALT 267

Query: 1056 YNSESYIKA---HNNISNEMLG----IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 1108
               ES  K+   +  +  E++     +      IE+L   ++  + ++  +E ++L +  
Sbjct: 268  AGEESTDKSEQVYEELRRELVTLVEQVHLHNNRIEELVAQIKVHVQRLNTLEGRMLRLA- 326

Query: 1109 NKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDI 1167
              C + R  F+  +   E++  W+D    +    +  +  R++  +  L+  L  L  + 
Sbjct: 327  ESCKITRDDFLLKYRNREMDPTWIDFICTLPGKGWKTLTTRHLEQLHSLRGDLSALAHET 386

Query: 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 1227
             LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 387  GLPVGEFRRVYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 446

Query: 1228 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 1287
            LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA+TIRIPVHMIETINK+ R SRQ+L
Sbjct: 447  LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRTSRQML 506

Query: 1288 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 1347
             E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+  + P
Sbjct: 507  HEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIP 566

Query: 1348 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407
             DAA+  ++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTRERIRQIE
Sbjct: 567  LDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIE 626

Query: 1408 AKALRKLRHPSRYYKLKIFLE 1428
            AKALRKL+HPSR  KL+ FL+
Sbjct: 627  AKALRKLKHPSRSRKLRSFLD 647



 Score =  484 bits (1247), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 275/608 (45%), Positives = 378/608 (62%), Gaps = 28/608 (4%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K LI  G+ERG++TF E+N  LP+D +  E IE ++     M I V E+    E     
Sbjct: 30  VKRLIAKGRERGHITFDELNAVLPQDQMSSEQIEDVMAALSEMGIQVLENEEQDEPETAQ 89

Query: 103 NITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGL 161
           +  + ++ EE+ E     +D++   RT DP++MY+REMGSVELL+R+GEI IAKRIE G 
Sbjct: 90  D-EAKEEAEESDEPQGGNIDAEAASRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGR 148

Query: 162 KDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEEK 221
            +MI  +   P TI  I+   +++   E+ + +IVD    ++        +G + +    
Sbjct: 149 DEMIGGLCESPLTIRAIISWHERLKDGEMLLRDIVDLEASQSGGPGPEDEEGEEGDEPAD 208

Query: 222 ILI------------ESSSADLSTEQLEKLKYESLIKFSNISFHFDKMR----KAFEKEG 265
                          E S   LS  + EKLK E L +F  I   + K+R    K  E   
Sbjct: 209 DDSDDDAEDGDGEQQEGSGLSLSALE-EKLKPEILARFEAIEPLYHKLRQLQTKRLEALT 267

Query: 266 YNSESYIKA---HNNISNEMLG----IRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVV 318
              ES  K+   +  +  E++     +      IE+L   ++  + ++  +E ++L +  
Sbjct: 268 AGEESTDKSEQVYEELRRELVTLVEQVHLHNNRIEELVAQIKVHVQRLNTLEGRMLRLA- 326

Query: 319 NKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDI 377
             C + R  F+  +   E++  W+D    +    +  +  R++  +  L+  L  L  + 
Sbjct: 327 ESCKITRDDFLLKYRNREMDPTWIDFICTLPGKGWKTLTTRHLEQLHSLRGDLSALAHET 386

Query: 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIG 437
            LP+ + R +   +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIG
Sbjct: 387 GLPVGEFRRVYATISRGERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 446

Query: 438 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQIL 497
           LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA+TIRIPVHMIETINK+ R SRQ+L
Sbjct: 447 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAKTIRIPVHMIETINKLVRTSRQML 506

Query: 498 QETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAP 557
            E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGDFIED+  + P
Sbjct: 507 HEIGREPAPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKTAVIP 566

Query: 558 SDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617
            DAA+  ++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF+VTRERIRQIE
Sbjct: 567 LDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIE 626

Query: 618 AKALRKLR 625
           AKALRKL+
Sbjct: 627 AKALRKLK 634


>gi|421253672|ref|ZP_15708805.1| RNA polymerase sigma factor RpoD, partial [Pasteurella multocida
            subsp. multocida str. Anand1_buffalo]
 gi|401693759|gb|EJS87715.1| RNA polymerase sigma factor RpoD, partial [Pasteurella multocida
            subsp. multocida str. Anand1_buffalo]
          Length = 539

 Score =  501 bits (1291), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 269/535 (50%), Positives = 357/535 (66%), Gaps = 23/535 (4%)

Query: 914  DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 973
            + GRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG+ ++  AI+  P  I  +L    
Sbjct: 7    EIGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAIAFYPEAISYLLDQYA 66

Query: 974  KISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKILIESSSADLSTEQLEKLKY 1031
             + +  +++ +++ G +D N  +   V  I+   + +E+    +S SA L+ E+ E+ + 
Sbjct: 67   LVEEGGVRLADLITGFVDPNAMTEGDVAEIEDTFDEDEDS---DSVSATLNEEEEEEEES 123

Query: 1032 ESLI------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 1073
            E                     KF  +     K     EK G  S+        +++   
Sbjct: 124  EEESTTDDSDSDNSIDPEVAREKFLELKTQHAKAVAMIEKHGRTSKKSKDQIQALADVFT 183

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
              R   K  + L + + N +  V   E+ I +IVV+K  MP+  F KVF  +E    W+ 
Sbjct: 184  QFRLVPKQFDTLVNLMSNMMKSVRLQERSIQKIVVDKAKMPKEQFQKVFIGHENKDTWLV 243

Query: 1134 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 1193
                    ++  L ++   I+     ++ ++    L ++ +R++  ++ AGE+KAR+AK+
Sbjct: 244  KALSSGKTWSEKLAKHEEEIRYYIDNILEIERQTNLTVSQIREVCERISAGELKARRAKK 303

Query: 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253
            EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 304  EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 363

Query: 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 1313
            AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK+
Sbjct: 364  AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 423

Query: 1314 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 1373
            +KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+K
Sbjct: 424  LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAK 483

Query: 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR   L+ FL+
Sbjct: 484  VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFLD 538



 Score =  487 bits (1253), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 262/522 (50%), Positives = 348/522 (66%), Gaps = 23/522 (4%)

Query: 124 DFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAAD 183
           + GRT DP++MYMREMGSVELLTR+GEI+IAKRIEEG+ ++  AI+  P  I  +L    
Sbjct: 7   EIGRTTDPVRMYMREMGSVELLTREGEIDIAKRIEEGINEVQSAIAFYPEAISYLLDQYA 66

Query: 184 KISKNEIKIDEIVDGLIDKNFSSNNRV--IKGNKNNNEEKILIESSSADLSTEQLEKLKY 241
            + +  +++ +++ G +D N  +   V  I+   + +E+    +S SA L+ E+ E+ + 
Sbjct: 67  LVEEGGVRLADLITGFVDPNAMTEGDVAEIEDTFDEDEDS---DSVSATLNEEEEEEEES 123

Query: 242 ESLI------------------KFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEML 283
           E                     KF  +     K     EK G  S+        +++   
Sbjct: 124 EEESTTDDSDSDNSIDPEVAREKFLELKTQHAKAVAMIEKHGRTSKKSKDQIQALADVFT 183

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
             R   K  + L + + N +  V   E+ I +IVV+K  MP+  F KVF  +E    W+ 
Sbjct: 184 QFRLVPKQFDTLVNLMSNMMKSVRLQERSIQKIVVDKAKMPKEQFQKVFIGHENKDTWLV 243

Query: 344 NETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKR 403
                   ++  L ++   I+     ++ ++    L ++ +R++  ++ AGE+KAR+AK+
Sbjct: 244 KALSSGKTWSEKLAKHEEEIRYYIDNILEIERQTNLTVSQIREVCERISAGELKARRAKK 303

Query: 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463
           EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ
Sbjct: 304 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 363

Query: 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523
           AITRSIADQARTIRIPVHMIETINK++RISRQ+LQE G E  P  +A +M MPE+KIRK+
Sbjct: 364 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREASPEELAERMGMPEDKIRKV 423

Query: 524 MKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESK 583
           +KIAKEP+SME+P+GDD+DSHLGDFIED  +  P D+A   S++    ++L  LTPRE+K
Sbjct: 424 LKIAKEPISMETPIGDDDDSHLGDFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAK 483

Query: 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           VLRMRFGI+M++DHTLEEVGKQFDVTRERIRQIEAKALRKLR
Sbjct: 484 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 525


>gi|338708468|ref|YP_004662669.1| RNA polymerase sigma-70 subunit RpoD [Zymomonas mobilis subsp.
            pomaceae ATCC 29192]
 gi|336295272|gb|AEI38379.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
            pomaceae ATCC 29192]
          Length = 667

 Score =  500 bits (1288), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 287/639 (44%), Positives = 399/639 (62%), Gaps = 47/639 (7%)

Query: 836  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 895
             +   K+RGY+T+ ++N+ LP+D +  E IE I+     M +++ E+    E        
Sbjct: 29   FVTQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGVNIVENEDAGEDGQSEEEG 88

Query: 896  SDD-DVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
            +++   +E T A  + V  +   RT DP++MY+REMG+VELL+R+GEI IAKRIE G   
Sbjct: 89   AEELQGDEGTPAPATVVKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDT 148

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-------GLIDKNF-----------S 995
            MI  +   P T   I+  +D +++  +++ EI+D       G   + F           S
Sbjct: 149  MILGLCESPITFDAIIEWSDALNEGTLQLREIIDLDAMLSQGPSPEQFEDEDDDNDNEIS 208

Query: 996  SNN----------RVIKGNKNNNEEKILIES----SSADLSTEQLE-KLKYESLIKFSNI 1040
              N             +G  + N ++I  ES        LS  Q+E +LK  SL KFS I
Sbjct: 209  ERNAGPTFKEDDEDEEEGELDENGQRIHRESIDDEDENTLSLAQMEEQLKPASLEKFSKI 268

Query: 1041 S--------FHFDKMRKAFEKEGYNSE---SYIKAHNNISNEMLGIRFTAKSIEKLCDTL 1089
            +           ++M+     E + ++   +Y +    ++ E+  ++F    IE L + L
Sbjct: 269  TDLYRQFSTLQSERMKALSVNEDFPTDKENAYQQLREELTAEVESVKFHNAKIEFLVEQL 328

Query: 1090 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 1149
                +++  +  Q+L +   +  +PR  F+  +  +E+   W+D  TKI   +       
Sbjct: 329  YTFNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGHEMEEGWIDRVTKIDKKWANFTANE 387

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
            +  I++++ ++ ++     + L +LR I   +  GE +AR AK EM EANLRLVISIAKK
Sbjct: 388  VEHIEQIRSEVADIAQITGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKK 447

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 448  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 507

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+E+P+GD
Sbjct: 508  VHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGD 567

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            +EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M++DHTL
Sbjct: 568  EEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTL 627

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 628  EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 666



 Score =  484 bits (1246), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 280/626 (44%), Positives = 389/626 (62%), Gaps = 47/626 (7%)

Query: 46  LIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNIT 105
            +   K+RGY+T+ ++N+ LP+D +  E IE I+     M +++ E+    E        
Sbjct: 29  FVTQAKKRGYVTYDQLNEALPQDQMSSEQIEDIMSALSEMGVNIVENEDAGEDGQSEEEG 88

Query: 106 SDD-DVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
           +++   +E T A  + V  +   RT DP++MY+REMG+VELL+R+GEI IAKRIE G   
Sbjct: 89  AEELQGDEGTPAPATVVKKETSDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRDT 148

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-------GLIDKNF-----------S 205
           MI  +   P T   I+  +D +++  +++ EI+D       G   + F           S
Sbjct: 149 MILGLCESPITFDAIIEWSDALNEGTLQLREIIDLDAMLSQGPSPEQFEDEDDDNDNEIS 208

Query: 206 SNN----------RVIKGNKNNNEEKILIES----SSADLSTEQLE-KLKYESLIKFSNI 250
             N             +G  + N ++I  ES        LS  Q+E +LK  SL KFS I
Sbjct: 209 ERNAGPTFKEDDEDEEEGELDENGQRIHRESIDDEDENTLSLAQMEEQLKPASLEKFSKI 268

Query: 251 S--------FHFDKMRKAFEKEGYNSE---SYIKAHNNISNEMLGIRFTAKSIEKLCDTL 299
           +           ++M+     E + ++   +Y +    ++ E+  ++F    IE L + L
Sbjct: 269 TDLYRQFSTLQSERMKALSVNEDFPTDKENAYQQLREELTAEVESVKFHNAKIEFLVEQL 328

Query: 300 RNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRN 359
               +++  +  Q+L +   +  +PR  F+  +  +E+   W+D  TKI   +       
Sbjct: 329 YTFNSRLRTLNGQMLRLA-ERYKVPRDSFLNAYLGHEMEEGWIDRVTKIDKKWANFTANE 387

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
           +  I++++ ++ ++     + L +LR I   +  GE +AR AK EM EANLRLVISIAKK
Sbjct: 388 VEHIEQIRSEVADIAQITGMTLKELRRIVTMVQKGEREARIAKTEMVEANLRLVISIAKK 447

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 448 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 507

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINK+ R SRQIL E G EP P  +A ++ MP EK+RK+MKIAKEP+S+E+P+GD
Sbjct: 508 VHMIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPIGD 567

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           +EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE +VLRMRFGI M++DHTL
Sbjct: 568 EEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTL 627

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 628 EEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|220927258|ref|YP_002502560.1| RNA polymerase sigma factor RpoD [Methylobacterium nodulans ORS 2060]
 gi|219951865|gb|ACL62257.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium nodulans ORS
            2060]
          Length = 665

 Score =  500 bits (1288), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 284/645 (44%), Positives = 406/645 (62%), Gaps = 60/645 (9%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 890
             K +IKL K+RGY+T+ E+N+ LP++    E IE ++     + ++V  +E   D +   
Sbjct: 31   VKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQLSELGVNVVEAEEADDNQAEG 90

Query: 891  LSNITSDDD-VEEATEAA-----------LSTVDSDFGRTKDPIKMYMREMGSVELLTRD 938
                 ++D+ V E TE A             T      RT DP++MY+REMGSVELL+R+
Sbjct: 91   AGEGGAEDEEVSEGTEVAEVAQNRPAVLRTETTKEPTDRTDDPVRMYLREMGSVELLSRE 150

Query: 939  GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-N 997
            GEI IAKRIE G + MI  +   P T   I+I  D++    + + +I+D  ++  ++  +
Sbjct: 151  GEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVDGRVLLRDIID--LEATYAGPD 208

Query: 998  NRVI----------------------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 1035
             R                        +G++++ E  + + +  A+L    LE        
Sbjct: 209  GRGGPAEGEEEGEGEAPEGEVPPPEGEGDEDDLENNVSLSAMEAELKPRVLE-------- 260

Query: 1036 KFSNISFHFDKMR--KAFEKE-----GYNSESYIKAHNNISNEMLG----IRFTAKSIEK 1084
             F  I+ ++ K+R  +A + E     G  SE+  + ++ + + ++     +   A  IE 
Sbjct: 261  TFDAIAENYRKLRNVQAEQAETRLQGGGASEAQGRQYSELKSRIVADVKSLSLNANRIEA 320

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYN 1143
            L + L +   ++   E +++ +     G+ R  F++ +   E++ +WV+   K+    + 
Sbjct: 321  LVEQLYDINKRLISQEGRLMRL-AESHGVARDEFLRHYQGYELDPHWVERVGKLGGKGWK 379

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
              + R    I+ L++++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLV
Sbjct: 380  NFVERGADGIQSLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLV 439

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 440  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 499

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 500  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 559

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+P+GD+EDSHLGDFIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M
Sbjct: 560  ETPIGDEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGM 619

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 620  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 664



 Score =  483 bits (1243), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 276/632 (43%), Positives = 396/632 (62%), Gaps = 60/632 (9%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISV--SEHVLDTETLM 100
            K +IKL K+RGY+T+ E+N+ LP++    E IE ++     + ++V  +E   D +   
Sbjct: 31  VKRMIKLAKKRGYVTYDELNEVLPQEEFTSEQIEDVLGQLSELGVNVVEAEEADDNQAEG 90

Query: 101 LSNITSDDD-VEEATEAA-----------LSTVDSDFGRTKDPIKMYMREMGSVELLTRD 148
                ++D+ V E TE A             T      RT DP++MY+REMGSVELL+R+
Sbjct: 91  AGEGGAEDEEVSEGTEVAEVAQNRPAVLRTETTKEPTDRTDDPVRMYLREMGSVELLSRE 150

Query: 149 GEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSS-N 207
           GEI IAKRIE G + MI  +   P T   I+I  D++    + + +I+D  ++  ++  +
Sbjct: 151 GEIAIAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVDGRVLLRDIID--LEATYAGPD 208

Query: 208 NRVI----------------------KGNKNNNEEKILIESSSADLSTEQLEKLKYESLI 245
            R                        +G++++ E  + + +  A+L    LE        
Sbjct: 209 GRGGPAEGEEEGEGEAPEGEVPPPEGEGDEDDLENNVSLSAMEAELKPRVLE-------- 260

Query: 246 KFSNISFHFDKMR--KAFEKE-----GYNSESYIKAHNNISNEMLG----IRFTAKSIEK 294
            F  I+ ++ K+R  +A + E     G  SE+  + ++ + + ++     +   A  IE 
Sbjct: 261 TFDAIAENYRKLRNVQAEQAETRLQGGGASEAQGRQYSELKSRIVADVKSLSLNANRIEA 320

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYN 353
           L + L +   ++   E +++ +     G+ R  F++ +   E++ +WV+   K+    + 
Sbjct: 321 LVEQLYDINKRLISQEGRLMRL-AESHGVARDEFLRHYQGYELDPHWVERVGKLGGKGWK 379

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
             + R    I+ L++++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLV
Sbjct: 380 NFVERGADGIQSLREQIMSLASETGLEIQEYRKIVHMVQKGEREARQAKKEMIEANLRLV 439

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 440 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 499

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 500 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 559

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+P+GD+EDSHLGDFIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M
Sbjct: 560 ETPIGDEEDSHLGDFIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGM 619

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 620 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 651


>gi|163843732|ref|YP_001628136.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
 gi|163674455|gb|ABY38566.1| RNA polymerase sigma factor RpoD [Brucella suis ATCC 23445]
          Length = 666

 Score =  500 bits (1287), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/639 (45%), Positives = 402/639 (62%), Gaps = 47/639 (7%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATEAALSTV---DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 949
               +DD+ EE    A++T         RT DP++MY+REMGSVELL+R+GEI IAKRIE 
Sbjct: 88   EEGNDDEAEEGGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEA 147

Query: 950  GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD----------------GLIDKN 993
            G + MI  +   P +   I+I  D+++++ I + EI+D                  +++ 
Sbjct: 148  GRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVIERVEEE 207

Query: 994  FSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIKFSNISF 1042
               + R  + ++++++          E    +   A+LS   +E +L+ + +     I+ 
Sbjct: 208  KPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMETLDFIAD 267

Query: 1043 HFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEKLCDTLR 1090
             + K+RK  +++        G  S S  + +  + ++++     +      IE+L + L 
Sbjct: 268  TYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLY 327

Query: 1091 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRN 1149
            +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     +     + 
Sbjct: 328  DINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKE 386

Query: 1150 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 1209
              SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLVISIAKK
Sbjct: 387  ADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKK 446

Query: 1210 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269
            YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 447  YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 506

Query: 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329
            VHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+PVGD
Sbjct: 507  VHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGD 566

Query: 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 1389
            +EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M++DHTL
Sbjct: 567  EEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTL 626

Query: 1390 EEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665



 Score =  483 bits (1242), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 283/626 (45%), Positives = 392/626 (62%), Gaps = 47/626 (7%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATEAALSTV---DSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEE 159
              +DD+ EE    A++T         RT DP++MY+REMGSVELL+R+GEI IAKRIE 
Sbjct: 88  EEGNDDEAEEGGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEA 147

Query: 160 GLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD----------------GLIDKN 203
           G + MI  +   P +   I+I  D+++++ I + EI+D                  +++ 
Sbjct: 148 GRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVIERVEEE 207

Query: 204 FSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIKFSNISF 252
              + R  + ++++++          E    +   A+LS   +E +L+ + +     I+ 
Sbjct: 208 KPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMETLDFIAD 267

Query: 253 HFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEKLCDTLR 300
            + K+RK  +++        G  S S  + +  + ++++     +      IE+L + L 
Sbjct: 268 TYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQLVEQLY 327

Query: 301 NQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRN 359
           +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     +     + 
Sbjct: 328 DINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWKEFAAKE 386

Query: 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKK 419
             SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLVISIAKK
Sbjct: 387 ADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLVISIAKK 446

Query: 420 YTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479
           YT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP
Sbjct: 447 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 506

Query: 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539
           VHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+PVGD
Sbjct: 507 VHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGD 566

Query: 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTL 599
           +EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M++DHTL
Sbjct: 567 EEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTL 626

Query: 600 EEVGKQFDVTRERIRQIEAKALRKLR 625
           EEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 EEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|328542886|ref|YP_004302995.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
 gi|326412632|gb|ADZ69695.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 666

 Score =  500 bits (1287), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 282/643 (43%), Positives = 398/643 (61%), Gaps = 55/643 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IK  K+RGY+T+ E+N+ LP + +  E IE  +     M I    +V+D++ +  +
Sbjct: 31   VKRMIKAAKKRGYVTYDELNEVLPSEQVSSEQIEDTMSMLSDMGI----NVIDSDEVDEA 86

Query: 893  NITSDDDVEE------ATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
             I   DD  +         A  +T      RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 87   AIDDGDDGSDLVPSGGTAVAKTTTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKR 146

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------- 995
            IE G + MI  +   P T   I+I  D++++ ++ + +I+D  ++  ++           
Sbjct: 147  IEAGREAMIAGLCESPLTFQAIIIWRDELNEGKVLLRDIID--LEATYAGPDAKAGPAGG 204

Query: 996  ---------SNNRVIKGNKNNNEE---------KILIESSSADLSTEQLEKLKYESLIKF 1037
                     +  R    + +++E          +     ++  LS  + E LK + L  F
Sbjct: 205  DGEEDEEGETEKRAPAASGDDSERGAEGEGEEDEEDEFETNVSLSAMEAE-LKPQVLETF 263

Query: 1038 SNISFHFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLC 1086
              ++  + K+R+  ++   N              Y K  + I  ++  +      I+ L 
Sbjct: 264  DRVADSYKKLRRLQDQLVENKLANRTLSPSQERRYKKLKDEIVVDVKSLSLNQNRIDALV 323

Query: 1087 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLI 1145
            + L +   ++   E ++L +  +  G+ R  F+K +   E++ NW+     +    +   
Sbjct: 324  EQLYDINKRLMGYEGRLLRLA-DSHGVDRTDFLKQYQGAELDPNWLRKVANLATRGWKNF 382

Query: 1146 LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 1205
            + +   +I+EL+Q++  L T+  L + + R I   +  GE +AR AK+EM EANLRLVIS
Sbjct: 383  VAKEKDTIRELRQEIQTLATETGLEITEFRKIVAMVQKGEREARIAKKEMVEANLRLVIS 442

Query: 1206 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 1265
            IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 443  IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 502

Query: 1266 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 1325
            IRIPVHMIETINKI R SRQ+L E G EP P  +A K++MP EK+RK++KIAKEP+S+E+
Sbjct: 503  IRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLET 562

Query: 1326 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 1385
            P+GD+EDSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++
Sbjct: 563  PIGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 622

Query: 1386 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 623  DHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665



 Score =  482 bits (1241), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 274/630 (43%), Positives = 388/630 (61%), Gaps = 55/630 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IK  K+RGY+T+ E+N+ LP + +  E IE  +     M I    +V+D++ +  +
Sbjct: 31  VKRMIKAAKKRGYVTYDELNEVLPSEQVSSEQIEDTMSMLSDMGI----NVIDSDEVDEA 86

Query: 103 NITSDDDVEE------ATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
            I   DD  +         A  +T      RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 87  AIDDGDDGSDLVPSGGTAVAKTTTTREPTDRTDDPVRMYLREMGSVELLSREGEIAIAKR 146

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFS----------- 205
           IE G + MI  +   P T   I+I  D++++ ++ + +I+D  ++  ++           
Sbjct: 147 IEAGREAMIAGLCESPLTFQAIIIWRDELNEGKVLLRDIID--LEATYAGPDAKAGPAGG 204

Query: 206 ---------SNNRVIKGNKNNNEE---------KILIESSSADLSTEQLEKLKYESLIKF 247
                    +  R    + +++E          +     ++  LS  + E LK + L  F
Sbjct: 205 DGEEDEEGETEKRAPAASGDDSERGAEGEGEEDEEDEFETNVSLSAMEAE-LKPQVLETF 263

Query: 248 SNISFHFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLC 296
             ++  + K+R+  ++   N              Y K  + I  ++  +      I+ L 
Sbjct: 264 DRVADSYKKLRRLQDQLVENKLANRTLSPSQERRYKKLKDEIVVDVKSLSLNQNRIDALV 323

Query: 297 DTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLI 355
           + L +   ++   E ++L +  +  G+ R  F+K +   E++ NW+     +    +   
Sbjct: 324 EQLYDINKRLMGYEGRLLRLA-DSHGVDRTDFLKQYQGAELDPNWLRKVANLATRGWKNF 382

Query: 356 LCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVIS 415
           + +   +I+EL+Q++  L T+  L + + R I   +  GE +AR AK+EM EANLRLVIS
Sbjct: 383 VAKEKDTIRELRQEIQTLATETGLEITEFRKIVAMVQKGEREARIAKKEMVEANLRLVIS 442

Query: 416 IAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 475
           IAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART
Sbjct: 443 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 502

Query: 476 IRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535
           IRIPVHMIETINKI R SRQ+L E G EP P  +A K++MP EK+RK++KIAKEP+S+E+
Sbjct: 503 IRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLET 562

Query: 536 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSS 595
           P+GD+EDSHLGDFIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++
Sbjct: 563 PIGDEEDSHLGDFIEDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNT 622

Query: 596 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 623 DHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|114328948|ref|YP_746105.1| RNA polymerase sigma factor RpoD [Granulibacter bethesdensis CGDNIH1]
 gi|114317122|gb|ABI63182.1| RNA polymerase sigma factor rpoD [Granulibacter bethesdensis CGDNIH1]
          Length = 654

 Score =  499 bits (1285), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 282/631 (44%), Positives = 389/631 (61%), Gaps = 44/631 (6%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI  GKERGY+TF E+N  LP +    E IE ++     M I V E     E+   + 
Sbjct: 31   KRLIARGKERGYITFDELNAVLPSEQNSSEQIEDVMANLSEMGIQVVESEETEESGEPAA 90

Query: 894  ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953
                 +  E  E + +  +   GRT DP++MY+REMGSVELL+R+GEI IAKRIE G   
Sbjct: 91   RAERAEETEDEERSGNVDEESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDM 150

Query: 954  MIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-----------------------GLI 990
            MI  +   P T   I+   +++   E+ + +I+D                          
Sbjct: 151  MIGGLCESPLTFRAIITWHERLKAGEMLLRDIIDLEATQGGPPPGVVEGGEEGAEEGEAD 210

Query: 991  DKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 1050
             + F+      +    ++ + I +  S+ +      EKLK E+L +F  I   + K+ K 
Sbjct: 211  AEAFTPPPPPEESEDGDDADGIGMSLSALE------EKLKPETLQRFEEIEAIYKKLSKM 264

Query: 1051 FEKE-----------GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ-VTQ 1098
              K              + ++Y K  + +  ++  +R     +E+L   L+ Q+NQ +T 
Sbjct: 265  QSKRLDSFTSGEEVTARSEKTYEKMRDELVAKVSEVRLHNGRVEELVLQLK-QLNQRLTG 323

Query: 1099 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQ 1157
            +E Q+L +    C +PR  F++    +E+  NW++  + +    +     R    + +++
Sbjct: 324  LEGQLLRLA-ESCKVPRDSFLEQHRNHELEPNWLERVSTLPGKAWKNFSARYPQEVGQIR 382

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             ++  +  D  LP+ +   + + +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 383  GRIGEVAADAGLPIPEFLRVYKTVNRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQF 442

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 443  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 502

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            K+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 503  KLVRTSRQMLHEIGREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 562

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED+  + P DAA+ A++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+
Sbjct: 563  FIEDKAAIIPLDAAIQANLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 622

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 623  VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 653



 Score =  482 bits (1240), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 274/618 (44%), Positives = 379/618 (61%), Gaps = 44/618 (7%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI  GKERGY+TF E+N  LP +    E IE ++     M I V E     E+   + 
Sbjct: 31  KRLIARGKERGYITFDELNAVLPSEQNSSEQIEDVMANLSEMGIQVVESEETEESGEPAA 90

Query: 104 ITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163
                +  E  E + +  +   GRT DP++MY+REMGSVELL+R+GEI IAKRIE G   
Sbjct: 91  RAERAEETEDEERSGNVDEESLGRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDM 150

Query: 164 MIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-----------------------GLI 200
           MI  +   P T   I+   +++   E+ + +I+D                          
Sbjct: 151 MIGGLCESPLTFRAIITWHERLKAGEMLLRDIIDLEATQGGPPPGVVEGGEEGAEEGEAD 210

Query: 201 DKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKA 260
            + F+      +    ++ + I +  S+ +      EKLK E+L +F  I   + K+ K 
Sbjct: 211 AEAFTPPPPPEESEDGDDADGIGMSLSALE------EKLKPETLQRFEEIEAIYKKLSKM 264

Query: 261 FEKE-----------GYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQ-VTQ 308
             K              + ++Y K  + +  ++  +R     +E+L   L+ Q+NQ +T 
Sbjct: 265 QSKRLDSFTSGEEVTARSEKTYEKMRDELVAKVSEVRLHNGRVEELVLQLK-QLNQRLTG 323

Query: 309 IEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPSIKELQ 367
           +E Q+L +    C +PR  F++    +E+  NW++  + +    +     R    + +++
Sbjct: 324 LEGQLLRLA-ESCKVPRDSFLEQHRNHELEPNWLERVSTLPGKAWKNFSARYPQEVGQIR 382

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            ++  +  D  LP+ +   + + +  GE  + +AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 383 GRIGEVAADAGLPIPEFLRVYKTVNRGERDSARAKKEMIEANLRLVISIAKKYTNRGLQF 442

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 443 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 502

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           K+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 503 KLVRTSRQMLHEIGREPQPEELAEKLGMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 562

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED+  + P DAA+ A++R     +L+SLTPRE +VLRMRFGI M++DHTLEEVG+QF+
Sbjct: 563 FIEDKAAIIPLDAAIQANLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 622

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKL+
Sbjct: 623 VTRERIRQIEAKALRKLK 640


>gi|170747007|ref|YP_001753267.1| RNA polymerase sigma factor RpoD [Methylobacterium radiotolerans JCM
            2831]
 gi|170653529|gb|ACB22584.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
            radiotolerans JCM 2831]
          Length = 659

 Score =  499 bits (1284), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 284/631 (45%), Positives = 394/631 (62%), Gaps = 38/631 (6%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL--- 889
             K ++KL K+RGY+T+ E+N+ LPE   D + +E ++     M I+V E     E     
Sbjct: 31   VKRMVKLAKKRGYVTYEEVNEVLPEGQSDPDQLEDVLSQLSEMGINVVEAEETDEAAGEK 90

Query: 890  -------MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
                           +       A  +T      RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 91   AADGEEEEAEGGEVAEVAPARAVAVATTTKEPTDRTDDPVRMYLREMGSVELLSREGEIA 150

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN---- 998
            IAKRIE G + MI  +   P T   I+I  D++ + ++ + +I+D  ++  ++  +    
Sbjct: 151  IAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVEGKVLLRDIID--LEATYAGPDGKNA 208

Query: 999  -RVIKGNKNNNEEKILIESSSAD-------LSTEQLE-KLKYESLIKFSNISFHFDKMRK 1049
             ++ +G ++ + E         D       +S   +E ++K   L  F  I+ ++ K+RK
Sbjct: 209  PQLAEGEESEDGEPPAPPEGGDDEDDLENNVSLAAMEAEIKPRVLETFDAIAANYRKLRK 268

Query: 1050 AFEKEGYN----SESYIKAHNNISNEMLGIRFT-AKSIEKLCDTLRNQINQVTQIEKQI- 1103
             F+ EG       E    A +    E+  I     KS+    + +   + Q+  I KQ+ 
Sbjct: 269  -FQIEGTERKAAGEQNTPAQDQKQAELKDIVVADVKSLSLNNNRIEALVGQLYSINKQLI 327

Query: 1104 -----LEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPSIKELQ 1157
                 L       G+ R  F++ +   E++ NW++   T     +  ++ R    + EL+
Sbjct: 328  GHEGRLMRFAESHGVARDEFLRHYQGYELDPNWMERVGTLGGKGWKNLVERGSKQVAELR 387

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             ++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 388  AQILDLASETGLEIGEYRRIVNMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQF 447

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 448  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 507

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 508  KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 567

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 568  FIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 627

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 628  VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 658



 Score =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 276/618 (44%), Positives = 384/618 (62%), Gaps = 38/618 (6%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETL--- 99
            K ++KL K+RGY+T+ E+N+ LPE   D + +E ++     M I+V E     E     
Sbjct: 31  VKRMVKLAKKRGYVTYEEVNEVLPEGQSDPDQLEDVLSQLSEMGINVVEAEETDEAAGEK 90

Query: 100 -------MLSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
                          +       A  +T      RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 91  AADGEEEEAEGGEVAEVAPARAVAVATTTKEPTDRTDDPVRMYLREMGSVELLSREGEIA 150

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNN---- 208
           IAKRIE G + MI  +   P T   I+I  D++ + ++ + +I+D  ++  ++  +    
Sbjct: 151 IAKRIEAGREAMIAGLCESPLTFQAIIIWRDELVEGKVLLRDIID--LEATYAGPDGKNA 208

Query: 209 -RVIKGNKNNNEEKILIESSSAD-------LSTEQLE-KLKYESLIKFSNISFHFDKMRK 259
            ++ +G ++ + E         D       +S   +E ++K   L  F  I+ ++ K+RK
Sbjct: 209 PQLAEGEESEDGEPPAPPEGGDDEDDLENNVSLAAMEAEIKPRVLETFDAIAANYRKLRK 268

Query: 260 AFEKEGYN----SESYIKAHNNISNEMLGIRFT-AKSIEKLCDTLRNQINQVTQIEKQI- 313
            F+ EG       E    A +    E+  I     KS+    + +   + Q+  I KQ+ 
Sbjct: 269 -FQIEGTERKAAGEQNTPAQDQKQAELKDIVVADVKSLSLNNNRIEALVGQLYSINKQLI 327

Query: 314 -----LEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYNLILCRNIPSIKELQ 367
                L       G+ R  F++ +   E++ NW++   T     +  ++ R    + EL+
Sbjct: 328 GHEGRLMRFAESHGVARDEFLRHYQGYELDPNWMERVGTLGGKGWKNLVERGSKQVAELR 387

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            ++++L ++  L + + R I   +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 388 AQILDLASETGLEIGEYRRIVNMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQF 447

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 448 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 507

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 508 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 567

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED+N++ P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 568 FIEDKNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 627

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKL+
Sbjct: 628 VTRERIRQIEAKALRKLK 645


>gi|306844486|ref|ZP_07477075.1| RNA polymerase sigma factor RpoD [Brucella inopinata BO1]
 gi|306275097|gb|EFM56853.1| RNA polymerase sigma factor RpoD [Brucella inopinata BO1]
          Length = 672

 Score =  499 bits (1284), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 403/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    ++R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDDRPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1239), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 393/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    ++R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDDRPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|354593488|ref|ZP_09011531.1| RNA polymerase sigma factor RpoD [Commensalibacter intestini A911]
 gi|353672599|gb|EHD14295.1| RNA polymerase sigma factor RpoD [Commensalibacter intestini A911]
          Length = 667

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 286/642 (44%), Positives = 394/642 (61%), Gaps = 54/642 (8%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV-LDTETLMLS 892
            K LI  GKERGY+T  E+N  LP+D +  E IE ++  F  M+I + E+   + ++   S
Sbjct: 31   KKLISKGKERGYVTLDELNAILPQDKMSSEQIEDVMSAFSEMNIQIIENEETEDDSSDES 90

Query: 893  NITSDDDVEEA-------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 945
                D D E A       +E A+   +S  GRT DP++MY+REMG+VELL+R+GEI IAK
Sbjct: 91   GEEVDTDAEAAESDEDGESEGAVVAAESTAGRTDDPVRMYLREMGAVELLSREGEIAIAK 150

Query: 946  RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--------GLIDKNFSSN 997
            RIE G   MI  +   P T   I+   +++   ++ + +IVD           D +   N
Sbjct: 151  RIEAGRNQMIGGLCESPLTFKAIIGWHEQLKVGDVLLRDIVDLEATQTEYDQSDLSEMEN 210

Query: 998  NRVIKGNKNNNEEKILI--------------ESSSADLST-------------EQLEKLK 1030
            +  + G ++N+E                   E +S  LS              +++EK+ 
Sbjct: 211  SLSVSGAESNDENDSENENDEEGDESGEDSNEENSLSLSALEEKYKDEIFGHFDEIEKIY 270

Query: 1031 ---YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 1087
               Y+  ++  ++    +K+   FE E      Y    N +  E+  +   +  I+ L +
Sbjct: 271  TKLYQLQVQRLDVIQAGEKLTPVFENE------YEDLRNKLIIEVQQVHLQSSKIDFLVE 324

Query: 1088 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY-NLIL 1146
             L+    ++  +E  +L +   KC + R  F+  +   E+N +W+D    +   Y  L +
Sbjct: 325  QLKTVSKKLATLEGSMLRMA-EKCKISRDDFLSKYHGYELNPDWMDAVRGLPGKYWKLFV 383

Query: 1147 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 1206
             R    + + + ++  L   + LP+++ R +   +  GE  A +AK+EM EANLRLVISI
Sbjct: 384  ERYEDDVNKCRDEIAELSQRVGLPISEFRRVFSTVSYGERDASRAKKEMIEANLRLVISI 443

Query: 1207 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 1266
            AKKYT+ GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI
Sbjct: 444  AKKYTNCGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 503

Query: 1267 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 1326
            RIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E P
Sbjct: 504  RIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLEIP 563

Query: 1327 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 1386
            +GD+EDSHLGDFIED++ + P DAA+  ++R     +L SLTPRE +VLRMRFGI M++D
Sbjct: 564  IGDEEDSHLGDFIEDKSAVIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTD 623

Query: 1387 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            HTLEEVG+QF+VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 624  HTLEEVGQQFNVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 665



 Score =  481 bits (1238), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 278/629 (44%), Positives = 384/629 (61%), Gaps = 54/629 (8%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHV-LDTETLMLS 102
           K LI  GKERGY+T  E+N  LP+D +  E IE ++  F  M+I + E+   + ++   S
Sbjct: 31  KKLISKGKERGYVTLDELNAILPQDKMSSEQIEDVMSAFSEMNIQIIENEETEDDSSDES 90

Query: 103 NITSDDDVEEA-------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAK 155
               D D E A       +E A+   +S  GRT DP++MY+REMG+VELL+R+GEI IAK
Sbjct: 91  GEEVDTDAEAAESDEDGESEGAVVAAESTAGRTDDPVRMYLREMGAVELLSREGEIAIAK 150

Query: 156 RIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--------GLIDKNFSSN 207
           RIE G   MI  +   P T   I+   +++   ++ + +IVD           D +   N
Sbjct: 151 RIEAGRNQMIGGLCESPLTFKAIIGWHEQLKVGDVLLRDIVDLEATQTEYDQSDLSEMEN 210

Query: 208 NRVIKGNKNNNEEKILI--------------ESSSADLST-------------EQLEKLK 240
           +  + G ++N+E                   E +S  LS              +++EK+ 
Sbjct: 211 SLSVSGAESNDENDSENENDEEGDESGEDSNEENSLSLSALEEKYKDEIFGHFDEIEKIY 270

Query: 241 ---YESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCD 297
              Y+  ++  ++    +K+   FE E      Y    N +  E+  +   +  I+ L +
Sbjct: 271 TKLYQLQVQRLDVIQAGEKLTPVFENE------YEDLRNKLIIEVQQVHLQSSKIDFLVE 324

Query: 298 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDY-NLIL 356
            L+    ++  +E  +L +   KC + R  F+  +   E+N +W+D    +   Y  L +
Sbjct: 325 QLKTVSKKLATLEGSMLRMA-EKCKISRDDFLSKYHGYELNPDWMDAVRGLPGKYWKLFV 383

Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
            R    + + + ++  L   + LP+++ R +   +  GE  A +AK+EM EANLRLVISI
Sbjct: 384 ERYEDDVNKCRDEIAELSQRVGLPISEFRRVFSTVSYGERDASRAKKEMIEANLRLVISI 443

Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
           AKKYT+ GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI
Sbjct: 444 AKKYTNCGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 503

Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536
           RIPVHMIETINK+ R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E P
Sbjct: 504 RIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLEIP 563

Query: 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596
           +GD+EDSHLGDFIED++ + P DAA+  ++R     +L SLTPRE +VLRMRFGI M++D
Sbjct: 564 IGDEEDSHLGDFIEDKSAVIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTD 623

Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           HTLEEVG+QF+VTRERIRQIEAKALRKL+
Sbjct: 624 HTLEEVGQQFNVTRERIRQIEAKALRKLK 652


>gi|225852960|ref|YP_002733193.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|256263561|ref|ZP_05466093.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|384211844|ref|YP_005600926.1| RNA polymerase sigma factor RpoD [Brucella melitensis M5-90]
 gi|384408953|ref|YP_005597574.1| RNA polymerase sigma factor RpoD [Brucella melitensis M28]
 gi|384445515|ref|YP_005604234.1| RNA polymerase sigma factor RpoD [Brucella melitensis NI]
 gi|225641325|gb|ACO01239.1| RNA polymerase sigma factor RpoD [Brucella melitensis ATCC 23457]
 gi|263093589|gb|EEZ17614.1| RNA polymerase sigma factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409500|gb|ADZ66565.1| RNA polymerase sigma factor RpoD [Brucella melitensis M28]
 gi|326539207|gb|ADZ87422.1| RNA polymerase sigma factor RpoD [Brucella melitensis M5-90]
 gi|349743504|gb|AEQ09047.1| RNA polymerase sigma factor RpoD [Brucella melitensis NI]
          Length = 672

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 290/645 (44%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ + + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNVLLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 282/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ + + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNVLLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|62290370|ref|YP_222163.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 1 str. 9-941]
 gi|261315652|ref|ZP_05954849.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M163/99/10]
 gi|423166450|ref|ZP_17153153.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI435a]
 gi|423171175|ref|ZP_17157850.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI474]
 gi|423172743|ref|ZP_17159414.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI486]
 gi|423178564|ref|ZP_17165208.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI488]
 gi|423180605|ref|ZP_17167246.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI010]
 gi|423183737|ref|ZP_17170374.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI016]
 gi|423185323|ref|ZP_17171937.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI021]
 gi|62196502|gb|AAX74802.1| RpoD, RNA polymerase sigma-70 factor [Brucella abortus bv. 1 str.
            9-941]
 gi|261304678|gb|EEY08175.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M163/99/10]
 gi|374538509|gb|EHR10017.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI474]
 gi|374543934|gb|EHR15412.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI435a]
 gi|374544262|gb|EHR15739.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI486]
 gi|374545345|gb|EHR16808.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI488]
 gi|374548136|gb|EHR19588.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI010]
 gi|374548565|gb|EHR20013.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI016]
 gi|374560033|gb|EHR31416.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI021]
          Length = 672

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDC 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDC 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|265984525|ref|ZP_06097260.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306837542|ref|ZP_07470416.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
 gi|264663117|gb|EEZ33378.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 gi|306407378|gb|EFM63583.1| RNA polymerase sigma factor RpoD [Brucella sp. NF 2653]
          Length = 672

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEANSISRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEANSISRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|148559099|ref|YP_001259363.1| RNA polymerase sigma factor RpoD [Brucella ovis ATCC 25840]
 gi|148370356|gb|ABQ60335.1| RNA polymerase sigma-70 factor [Brucella ovis ATCC 25840]
          Length = 672

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLTMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLTMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|17986815|ref|NP_539449.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str. 16M]
 gi|23502348|ref|NP_698475.1| RNA polymerase sigma factor RpoD [Brucella suis 1330]
 gi|82700292|ref|YP_414866.1| RNA polymerase sigma factor RpoD [Brucella melitensis biovar Abortus
            2308]
 gi|161619426|ref|YP_001593313.1| RNA polymerase sigma factor RpoD [Brucella canis ATCC 23365]
 gi|189024598|ref|YP_001935366.1| RNA polymerase sigma factor RpoD [Brucella abortus S19]
 gi|237815873|ref|ZP_04594870.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|256369896|ref|YP_003107407.1| RNA polymerase sigma factor RpoD [Brucella microti CCM 4915]
 gi|260546908|ref|ZP_05822647.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260565297|ref|ZP_05835781.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260566021|ref|ZP_05836491.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260755199|ref|ZP_05867547.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260758418|ref|ZP_05870766.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260762244|ref|ZP_05874587.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
            86/8/59]
 gi|260884215|ref|ZP_05895829.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|261214461|ref|ZP_05928742.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str. Tulya]
 gi|261219607|ref|ZP_05933888.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261322495|ref|ZP_05961692.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261752768|ref|ZP_05996477.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|265991536|ref|ZP_06104093.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
            Rev.1]
 gi|265995374|ref|ZP_06107931.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
            Ether]
 gi|294852799|ref|ZP_06793472.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297248755|ref|ZP_06932473.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
            B3196]
 gi|306843169|ref|ZP_07475787.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
 gi|376272789|ref|YP_005151367.1| RNA polymerase sigma factor RpoD [Brucella abortus A13334]
 gi|376275909|ref|YP_005116348.1| RNA polymerase sigma factor RpoD [Brucella canis HSK A52141]
 gi|376281140|ref|YP_005155146.1| RNA polymerase sigma factor RpoD [Brucella suis VBI22]
 gi|384225134|ref|YP_005616298.1| RNA polymerase sigma factor RpoD [Brucella suis 1330]
 gi|423188458|ref|ZP_17175068.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI259]
 gi|17982448|gb|AAL51713.1| RNA polymerase sigma factor rpod [Brucella melitensis bv. 1 str. 16M]
 gi|23348329|gb|AAN30390.1| RNA polymerase sigma-70 factor [Brucella suis 1330]
 gi|82616393|emb|CAJ11454.1| Sigma-70 factor family:Sigma-70 factor, region 1.1:Sigma-70 region
            3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70,
            non-essent [Brucella melitensis biovar Abortus 2308]
 gi|161336237|gb|ABX62542.1| RNA polymerase sigma factor rpoD [Brucella canis ATCC 23365]
 gi|189020170|gb|ACD72892.1| RNA polymerase sigma factor [Brucella abortus S19]
 gi|237789171|gb|EEP63382.1| RNA polymerase sigma factor RpoD [Brucella abortus str. 2308 A]
 gi|256000059|gb|ACU48458.1| RNA polymerase sigma factor [Brucella microti CCM 4915]
 gi|260095958|gb|EEW79835.1| RNA polymerase sigma factor [Brucella abortus NCTC 8038]
 gi|260151365|gb|EEW86459.1| RNA polymerase sigma factor [Brucella melitensis bv. 1 str. 16M]
 gi|260155539|gb|EEW90619.1| RNA polymerase sigma factor [Brucella suis bv. 4 str. 40]
 gi|260668736|gb|EEX55676.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|260672676|gb|EEX59497.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
            86/8/59]
 gi|260675307|gb|EEX62128.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|260873743|gb|EEX80812.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|260916068|gb|EEX82929.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str. Tulya]
 gi|260924696|gb|EEX91264.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|261295185|gb|EEX98681.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|261742521|gb|EEY30447.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|262766487|gb|EEZ12276.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
            Ether]
 gi|263002320|gb|EEZ14895.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
            Rev.1]
 gi|294821388|gb|EFG38387.1| RNA polymerase primary sigma factor [Brucella sp. NVSL 07-0026]
 gi|297175924|gb|EFH35271.1| RNA polymerase primary sigma factor [Brucella abortus bv. 5 str.
            B3196]
 gi|306286647|gb|EFM58210.1| RNA polymerase sigma factor RpoD [Brucella sp. BO2]
 gi|343383314|gb|AEM18806.1| RNA polymerase sigma factor RpoD [Brucella suis 1330]
 gi|358258739|gb|AEU06474.1| RNA polymerase sigma factor RpoD [Brucella suis VBI22]
 gi|363400395|gb|AEW17365.1| RNA polymerase sigma factor RpoD [Brucella abortus A13334]
 gi|363404476|gb|AEW14771.1| RNA polymerase sigma factor RpoD [Brucella canis HSK A52141]
 gi|374559020|gb|EHR30409.1| RNA polymerase sigma factor rpoD [Brucella abortus bv. 1 str. NI259]
          Length = 672

 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|398386426|ref|ZP_10544427.1| RNA polymerase sigma factor, sigma-70 family [Sphingobium sp. AP49]
 gi|397718209|gb|EJK78801.1| RNA polymerase sigma factor, sigma-70 family [Sphingobium sp. AP49]
          Length = 683

 Score =  498 bits (1282), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/657 (44%), Positives = 400/657 (60%), Gaps = 68/657 (10%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 893
            K LI   K+RGY+T+ E+ND LP+D +  E IE I+     M +++ E+   +E     +
Sbjct: 32   KKLIARAKKRGYITYDELNDALPQDQMSSEQIEDIMSALNEMGVNIVENEEASE-----D 86

Query: 894  ITSDDDVEEATEAALSTVDSDFG-------------RTKDPIKMYMREMGSVELLTRDGE 940
                 + E+A +A   + D D G             RT DP++MY+REMG+VELL+R+GE
Sbjct: 87   GDEQREREDAEDAEDDSGDEDGGPKLVTEKKKETVDRTDDPVRMYLREMGAVELLSREGE 146

Query: 941  IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNN 998
            I IAKRIE G   MI  +   PTT   I+  +  ++  E+++ EI+D   ++ K+ +  N
Sbjct: 147  IAIAKRIEAGRDTMILGLCESPTTFNAIIEWSTALNNGEMQLREILDLDAMLSKDPAPEN 206

Query: 999  RVIKGNKNNNE--EKILIES---------SSAD------------------------LST 1023
                   ++ E  EK    S          SAD                        LS 
Sbjct: 207  LEEGAEDDDGEISEKTAGPSFKEEEEPEEESADGDEDEDGTERRARRNEEEEEEDNTLSL 266

Query: 1024 EQLEK-LKYESLIKFSNISFHFDKMRKAFEKEGY---NSES--------YIKAHNNISNE 1071
             Q+E+ LK  +L KF+ I+  F    KA E       N E+        Y +   +++ E
Sbjct: 267  AQMEETLKPMALEKFATITDIFRAFSKAQEARMLAMANGETLSQKAEDNYQELRESLTAE 326

Query: 1072 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 1131
            +  ++F  + IE L D L     ++T +  Q+L +   +  + R  F+  +  +E++  W
Sbjct: 327  VESVQFHQQKIEYLVDQLYAYNRRLTALGGQMLRLA-ERHKVSRKDFLDRYVNHELDDGW 385

Query: 1132 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 1191
            ++    +   +         +++ ++ ++  +     + L++ R I   +  GE +AR A
Sbjct: 386  MEKVQGLDKKWAAFAAAEGRAVERIRTEVGEIAQATGMSLSEFRRIVNMVQKGEREARIA 445

Query: 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251
            K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 446  KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 505

Query: 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 1311
            RQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+R
Sbjct: 506  RQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVR 565

Query: 1312 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371
            K+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE
Sbjct: 566  KVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPRE 625

Query: 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
             +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  K++ FL+
Sbjct: 626  ERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFLD 682



 Score =  481 bits (1239), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 284/644 (44%), Positives = 390/644 (60%), Gaps = 68/644 (10%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSN 103
           K LI   K+RGY+T+ E+ND LP+D +  E IE I+     M +++ E+   +E     +
Sbjct: 32  KKLIARAKKRGYITYDELNDALPQDQMSSEQIEDIMSALNEMGVNIVENEEASE-----D 86

Query: 104 ITSDDDVEEATEAALSTVDSDFG-------------RTKDPIKMYMREMGSVELLTRDGE 150
                + E+A +A   + D D G             RT DP++MY+REMG+VELL+R+GE
Sbjct: 87  GDEQREREDAEDAEDDSGDEDGGPKLVTEKKKETVDRTDDPVRMYLREMGAVELLSREGE 146

Query: 151 IEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD--GLIDKNFSSNN 208
           I IAKRIE G   MI  +   PTT   I+  +  ++  E+++ EI+D   ++ K+ +  N
Sbjct: 147 IAIAKRIEAGRDTMILGLCESPTTFNAIIEWSTALNNGEMQLREILDLDAMLSKDPAPEN 206

Query: 209 RVIKGNKNNNE--EKILIES---------SSAD------------------------LST 233
                  ++ E  EK    S          SAD                        LS 
Sbjct: 207 LEEGAEDDDGEISEKTAGPSFKEEEEPEEESADGDEDEDGTERRARRNEEEEEEDNTLSL 266

Query: 234 EQLEK-LKYESLIKFSNISFHFDKMRKAFEKEGY---NSES--------YIKAHNNISNE 281
            Q+E+ LK  +L KF+ I+  F    KA E       N E+        Y +   +++ E
Sbjct: 267 AQMEETLKPMALEKFATITDIFRAFSKAQEARMLAMANGETLSQKAEDNYQELRESLTAE 326

Query: 282 MLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNW 341
           +  ++F  + IE L D L     ++T +  Q+L +   +  + R  F+  +  +E++  W
Sbjct: 327 VESVQFHQQKIEYLVDQLYAYNRRLTALGGQMLRLA-ERHKVSRKDFLDRYVNHELDDGW 385

Query: 342 VDNETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKA 401
           ++    +   +         +++ ++ ++  +     + L++ R I   +  GE +AR A
Sbjct: 386 MEKVQGLDKKWAAFAAAEGRAVERIRTEVGEIAQATGMSLSEFRRIVNMVQKGEREARIA 445

Query: 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461
           K+EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI
Sbjct: 446 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 505

Query: 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521
           RQAITRSIADQARTIRIPVHMIETINK+ R SRQ L E G EP P  +A ++ MP EK+R
Sbjct: 506 RQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKVR 565

Query: 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 581
           K+MKIAKEP+S+E+P+GD+EDSHLGDFIED+N + P DAA+ A+++  V  +L SLTPRE
Sbjct: 566 KVMKIAKEPISLETPIGDEEDSHLGDFIEDKNAIIPVDAAIQANLKETVTRVLASLTPRE 625

Query: 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
            +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 626 ERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 669


>gi|225627926|ref|ZP_03785962.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|261222619|ref|ZP_05936900.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261758658|ref|ZP_06002367.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|265998584|ref|ZP_06111141.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|225617089|gb|EEH14135.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|260921203|gb|EEX87856.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|261738642|gb|EEY26638.1| RNA polymerase sigma factor [Brucella sp. F5/99]
 gi|262553208|gb|EEZ09042.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
          Length = 672

 Score =  498 bits (1282), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKKLKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKKLKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LVEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|323137010|ref|ZP_08072090.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC 49242]
 gi|322397771|gb|EFY00293.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocystis sp. ATCC 49242]
          Length = 670

 Score =  498 bits (1282), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 283/642 (44%), Positives = 393/642 (61%), Gaps = 50/642 (7%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH-----VLDTE 887
             K +IKL K+RG++T++E+N  LP + +  + IE +      M I+VSE      V   E
Sbjct: 32   VKRMIKLAKKRGFVTYAELNAVLPSEEVSSDQIEDVYAMLSEMGITVSEGDDPDDVEAEE 91

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                      D VE     A++T  S+   RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 92   QAEEEEGEGGDLVESPRSTAVATRTSEPADRTDDPVRMYLREMGSVELLSREGEIAIAKR 151

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 1006
            IE G + MI  +   P T   I+I  +++   ++ + +I+D  ++  ++  +    G  +
Sbjct: 152  IEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIID--LEATYAGPDGKAAGKTS 209

Query: 1007 NNEEKILIESS----------------------------SADLSTEQLEKLKYESLIKFS 1038
               E  +  ++                            S  LS  + E LK + L  F+
Sbjct: 210  GETEGEMAPATAPRTPPAGLSEEAAPPEEAFEEEEDMENSVSLSAMEAE-LKPKVLETFA 268

Query: 1039 NISFHFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCD 1087
             ++  + K+R+  ++   N              Y      I  ++  +      IE L +
Sbjct: 269  RVADAYKKLRRLQDQNVENKLKNETLTPAQERKYKTIKKEIVTDVKSLSLNQNRIEALVE 328

Query: 1088 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLIL 1146
             L +   ++   E ++L +  +  G+ R  FI  F  +E++  WV    +++   +   +
Sbjct: 329  QLYDINKRLIGYETKLLRLA-DSHGVAREDFIDKFHGSELDPKWVMRVAQLRSRGWKEFV 387

Query: 1147 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 1206
                  IK+L+ ++  L T+  L +++ R I   +  GE +AR+AK+EM EANLRLVISI
Sbjct: 388  AEEKDRIKDLRAEIHALATETGLEISEFRKIVHMVQKGEREARQAKKEMVEANLRLVISI 447

Query: 1207 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 1266
            AKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI
Sbjct: 448  AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 507

Query: 1267 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 1326
            RIPVHMIETINKI R SRQ+L E G EP P  ++ K+ MP EK+RK++KIAKEP+S+E+P
Sbjct: 508  RIPVHMIETINKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETP 567

Query: 1327 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 1386
            +GD+EDSHLGDFIED+N + P +AA+ +++R     +L SLTPRE +VLRMRFGI M++D
Sbjct: 568  IGDEEDSHLGDFIEDKNAVLPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTD 627

Query: 1387 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            HTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 628  HTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 669



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 275/629 (43%), Positives = 383/629 (60%), Gaps = 50/629 (7%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEH-----VLDTE 97
            K +IKL K+RG++T++E+N  LP + +  + IE +      M I+VSE      V   E
Sbjct: 32  VKRMIKLAKKRGFVTYAELNAVLPSEEVSSDQIEDVYAMLSEMGITVSEGDDPDDVEAEE 91

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                     D VE     A++T  S+   RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 92  QAEEEEGEGGDLVESPRSTAVATRTSEPADRTDDPVRMYLREMGSVELLSREGEIAIAKR 151

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKN 216
           IE G + MI  +   P T   I+I  +++   ++ + +I+D  ++  ++  +    G  +
Sbjct: 152 IEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIID--LEATYAGPDGKAAGKTS 209

Query: 217 NNEEKILIESS----------------------------SADLSTEQLEKLKYESLIKFS 248
              E  +  ++                            S  LS  + E LK + L  F+
Sbjct: 210 GETEGEMAPATAPRTPPAGLSEEAAPPEEAFEEEEDMENSVSLSAMEAE-LKPKVLETFA 268

Query: 249 NISFHFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCD 297
            ++  + K+R+  ++   N              Y      I  ++  +      IE L +
Sbjct: 269 RVADAYKKLRRLQDQNVENKLKNETLTPAQERKYKTIKKEIVTDVKSLSLNQNRIEALVE 328

Query: 298 TLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDYNLIL 356
            L +   ++   E ++L +  +  G+ R  FI  F  +E++  WV    +++   +   +
Sbjct: 329 QLYDINKRLIGYETKLLRLA-DSHGVAREDFIDKFHGSELDPKWVMRVAQLRSRGWKEFV 387

Query: 357 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISI 416
                 IK+L+ ++  L T+  L +++ R I   +  GE +AR+AK+EM EANLRLVISI
Sbjct: 388 AEEKDRIKDLRAEIHALATETGLEISEFRKIVHMVQKGEREARQAKKEMVEANLRLVISI 447

Query: 417 AKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 476
           AKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI
Sbjct: 448 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 507

Query: 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536
           RIPVHMIETINKI R SRQ+L E G EP P  ++ K+ MP EK+RK++KIAKEP+S+E+P
Sbjct: 508 RIPVHMIETINKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETP 567

Query: 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596
           +GD+EDSHLGDFIED+N + P +AA+ +++R     +L SLTPRE +VLRMRFGI M++D
Sbjct: 568 IGDEEDSHLGDFIEDKNAVLPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTD 627

Query: 597 HTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           HTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 628 HTLEEVGQQFSVTRERIRQIEAKALRKLK 656


>gi|221236078|ref|YP_002518515.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus NA1000]
 gi|220965251|gb|ACL96607.1| RNA polymerase sigma factor rpoD [Caulobacter crescentus NA1000]
          Length = 653

 Score =  498 bits (1282), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 281/631 (44%), Positives = 393/631 (62%), Gaps = 42/631 (6%)

Query: 831  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 890
            KKF   IK  K RGY+T  E+N  LP + +  + IE  +     M ++V E   D E   
Sbjct: 31   KKF---IKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAENAE 87

Query: 891  LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 950
               + + D   E T    S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 88   GGEVATRD---ENTTVIASDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 144

Query: 951  LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 1010
               MI  +     T   I++  +++    I + E++D  ++  +++ N V       ++E
Sbjct: 145  RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYAAINGVAAQPAAEDDE 202

Query: 1011 KIL--IESSSADLSTEQLE--------------------KLKYESLIKFSNISFHFDKMR 1048
                 ++  + +   E  E                    +L+   +     I+  F+  R
Sbjct: 203  GPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFEAFR 262

Query: 1049 KAFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVT 1097
            K  +K      +G + S++  KA+  +S  ++     ++     IE L + L     ++ 
Sbjct: 263  KLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLI 322

Query: 1098 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 1157
             +E ++L +  +  G+ R  F+K +  +E+N  W +    +   +   +  +  S+ +++
Sbjct: 323  GLEGRLLRLA-DSYGISRGEFLKAYFGSELNPTWSEQVKAMGVRWTKFVENDSQSVTDIR 381

Query: 1158 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 1217
             ++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 382  SEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 441

Query: 1218 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 1277
            LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 442  LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 501

Query: 1278 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337
            KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 502  KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 561

Query: 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397
            FIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 562  FIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 621

Query: 1398 VTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 622  VTRERIRQIEAKALRKLKHPSRSRKLRSFLD 652



 Score =  480 bits (1236), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 273/618 (44%), Positives = 383/618 (61%), Gaps = 42/618 (6%)

Query: 41  KKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLM 100
           KKF   IK  K RGY+T  E+N  LP + +  + IE  +     M ++V E   D E   
Sbjct: 31  KKF---IKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAENAE 87

Query: 101 LSNITSDDDVEEATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEG 160
              + + D   E T    S   + + RT DP++MY+REMGSVELL+R+GEI IAKRIE G
Sbjct: 88  GGEVATRD---ENTTVIASDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 144

Query: 161 LKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSNNRVIKGNKNNNEE 220
              MI  +     T   I++  +++    I + E++D  ++  +++ N V       ++E
Sbjct: 145 RDTMIRGLCESALTFEAIMVWREELGTGRILLREVID--LEGTYAAINGVAAQPAAEDDE 202

Query: 221 KIL--IESSSADLSTEQLE--------------------KLKYESLIKFSNISFHFDKMR 258
                ++  + +   E  E                    +L+   +     I+  F+  R
Sbjct: 203 GPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFEAFR 262

Query: 259 KAFEK------EGYN-SESYIKAHNNISNEML----GIRFTAKSIEKLCDTLRNQINQVT 307
           K  +K      +G + S++  KA+  +S  ++     ++     IE L + L     ++ 
Sbjct: 263 KLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLI 322

Query: 308 QIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQ 367
            +E ++L +  +  G+ R  F+K +  +E+N  W +    +   +   +  +  S+ +++
Sbjct: 323 GLEGRLLRLA-DSYGISRGEFLKAYFGSELNPTWSEQVKAMGVRWTKFVENDSQSVTDIR 381

Query: 368 QKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQF 427
            ++  L T+  +P++D R I + +  GE +AR+AK+EM EANLRLVISIAKKYT+RGLQF
Sbjct: 382 SEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 441

Query: 428 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 487
           LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN
Sbjct: 442 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 501

Query: 488 KISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547
           KI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+E+P+GD+EDSHLGD
Sbjct: 502 KIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGD 561

Query: 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607
           FIED+N + P DAA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLEEVG+QF 
Sbjct: 562 FIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFS 621

Query: 608 VTRERIRQIEAKALRKLR 625
           VTRERIRQIEAKALRKL+
Sbjct: 622 VTRERIRQIEAKALRKLK 639


>gi|296445787|ref|ZP_06887740.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
            OB3b]
 gi|296256767|gb|EFH03841.1| RNA polymerase, sigma 70 subunit, RpoD [Methylosinus trichosporium
            OB3b]
          Length = 669

 Score =  498 bits (1282), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 283/638 (44%), Positives = 395/638 (61%), Gaps = 45/638 (7%)

Query: 834  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE------HVLDTE 887
            K +IKL K+RG++T++E+N  LP + +  + IE +    + M I+VSE         + +
Sbjct: 33   KRMIKLAKKRGFVTYTELNAVLPSEEVSSDQIEDVYAMLQEMGITVSEGDDPDDAEGEEQ 92

Query: 888  TLMLSNITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKR 946
                   T  + VE A   A++T  S+   RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 93   QEEEEAETGGEVVESARATAVATRSSEPADRTDDPVRMYLREMGSVELLSREGEIAIAKR 152

Query: 947  IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------GLIDKNFSSN 997
            IE G + MI  +   P T   I+I  +++   ++ + +I+D         G   K  +  
Sbjct: 153  IEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIIDLEATYAGPEGKNAKPPAPQ 212

Query: 998  NRVIKGNKNNNEEKILIESS---------------SADLSTEQLEKLKYESLIKFSNISF 1042
            + +       +    L E                 S  LS  + E LK   L  F+ ++ 
Sbjct: 213  DDLAPATAPRSPPAALDEPGAPAEESFEEEDDLENSVSLSAMEAE-LKPRVLETFARVAD 271

Query: 1043 HFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 1091
             + K+R+  ++   N              Y +    I  ++  +      IE L + L +
Sbjct: 272  AYKKLRRLQDQNVENKLKNETLTPAQERKYKQLKKEIVTDVKSLSLNQNRIEALVEQLYD 331

Query: 1092 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYNLILCRNI 1150
               ++   E+++  ++ +  G+ R  FI  F  +E++  W++  +K+    +   +    
Sbjct: 332  INKRLVGYERKLF-MLADAQGVQREDFIDKFQGSELDPKWINRVSKLGSRGWKEFVANEK 390

Query: 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 1210
              I+EL+ ++  L T+  L + + R I + +  GE +AR+AK+EM EANLRLVISIAKKY
Sbjct: 391  DRIRELRGEIHALATETGLEIAEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKY 450

Query: 1211 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270
            T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 451  TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 510

Query: 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330
            HMIETINKI R SRQ+L E G EP P  ++ K+ MP EK+RK++KIAKEP+S+E+P+GD+
Sbjct: 511  HMIETINKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDE 570

Query: 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 1390
            EDSHLGDFIED+N + P +AA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLE
Sbjct: 571  EDSHLGDFIEDKNAILPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 630

Query: 1391 EVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            EVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 631  EVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 668



 Score =  481 bits (1237), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 275/625 (44%), Positives = 385/625 (61%), Gaps = 45/625 (7%)

Query: 44  KILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSE------HVLDTE 97
           K +IKL K+RG++T++E+N  LP + +  + IE +    + M I+VSE         + +
Sbjct: 33  KRMIKLAKKRGFVTYTELNAVLPSEEVSSDQIEDVYAMLQEMGITVSEGDDPDDAEGEEQ 92

Query: 98  TLMLSNITSDDDVEEATEAALSTVDSDFG-RTKDPIKMYMREMGSVELLTRDGEIEIAKR 156
                  T  + VE A   A++T  S+   RT DP++MY+REMGSVELL+R+GEI IAKR
Sbjct: 93  QEEEEAETGGEVVESARATAVATRSSEPADRTDDPVRMYLREMGSVELLSREGEIAIAKR 152

Query: 157 IEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------GLIDKNFSSN 207
           IE G + MI  +   P T   I+I  +++   ++ + +I+D         G   K  +  
Sbjct: 153 IEAGREAMIAGLCESPLTFQAIIIWREELEAGKVLLRDIIDLEATYAGPEGKNAKPPAPQ 212

Query: 208 NRVIKGNKNNNEEKILIESS---------------SADLSTEQLEKLKYESLIKFSNISF 252
           + +       +    L E                 S  LS  + E LK   L  F+ ++ 
Sbjct: 213 DDLAPATAPRSPPAALDEPGAPAEESFEEEDDLENSVSLSAMEAE-LKPRVLETFARVAD 271

Query: 253 HFDKMRKAFEKEGYN-----------SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRN 301
            + K+R+  ++   N              Y +    I  ++  +      IE L + L +
Sbjct: 272 AYKKLRRLQDQNVENKLKNETLTPAQERKYKQLKKEIVTDVKSLSLNQNRIEALVEQLYD 331

Query: 302 QINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI-QHDYNLILCRNI 360
              ++   E+++  ++ +  G+ R  FI  F  +E++  W++  +K+    +   +    
Sbjct: 332 INKRLVGYERKLF-MLADAQGVQREDFIDKFQGSELDPKWINRVSKLGSRGWKEFVANEK 390

Query: 361 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKY 420
             I+EL+ ++  L T+  L + + R I + +  GE +AR+AK+EM EANLRLVISIAKKY
Sbjct: 391 DRIRELRGEIHALATETGLEIAEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKY 450

Query: 421 TDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480
           T+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV
Sbjct: 451 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 510

Query: 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540
           HMIETINKI R SRQ+L E G EP P  ++ K+ MP EK+RK++KIAKEP+S+E+P+GD+
Sbjct: 511 HMIETINKIVRTSRQMLHEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPIGDE 570

Query: 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLE 600
           EDSHLGDFIED+N + P +AA+ +++R     +L SLTPRE +VLRMRFGI M++DHTLE
Sbjct: 571 EDSHLGDFIEDKNAILPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLE 630

Query: 601 EVGKQFDVTRERIRQIEAKALRKLR 625
           EVG+QF VTRERIRQIEAKALRKL+
Sbjct: 631 EVGQQFSVTRERIRQIEAKALRKLK 655


>gi|261325543|ref|ZP_05964740.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 gi|261301523|gb|EEY05020.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
          Length = 672

 Score =  498 bits (1282), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 291/645 (45%), Positives = 402/645 (62%), Gaps = 53/645 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 943
               +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88   EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 944  AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 987
            AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148  AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 988  GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 1036
              +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208  ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 1037 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 1084
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268  LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 1085 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 1143
            L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328  LIEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 1144 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 1203
                +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387  EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 1204 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263
            ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447  ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 1323
            RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507  RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 1324 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383
            E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567  ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            ++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 671



 Score =  480 bits (1236), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/632 (44%), Positives = 392/632 (62%), Gaps = 53/632 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATE---------AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEI 153
              +DD+ EE  +         A  +T      RT DP++MY+REMGSVELL+R+GEI I
Sbjct: 88  EEGNDDEAEEGGDLVEAGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIAI 147

Query: 154 AKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------------- 197
           AKRIE G + MI  +   P +   I+I  D+++++ I + EI+D                
Sbjct: 148 AKRIEAGRETMIAGLCESPLSFQAIIIWRDQLNESNILLREIIDLETTYAGPEAKQAPVI 207

Query: 198 GLIDKNFSSNNRVIKGNKNNNE----------EKILIESSSADLSTEQLE-KLKYESLIK 246
             +++    + R  + ++++++          E    +   A+LS   +E +L+ + +  
Sbjct: 208 ERVEEEKPRDERPQRRSRDDDDITNVGGDMPVEDDDDDEDEANLSLAAMEAELRPQVMET 267

Query: 247 FSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIEK 294
              I+  + K+RK  +++        G  S S  + +  + ++++     +      IE+
Sbjct: 268 LDFIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIEQ 327

Query: 295 LCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN-ETKIQHDYN 353
           L + L +   ++ Q E ++L +     G+ R  F+K +  +E++ NWV+   T     + 
Sbjct: 328 LIEQLYDINKRLVQNEGKLLRLA-ESFGVRREDFLKEYQGHELDPNWVERVATLPSRGWK 386

Query: 354 LILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLV 413
               +   SI  L+ ++ NL T+  + + + R I  ++  GE +A  AK+EM EANLRLV
Sbjct: 387 EFAAKEADSIGRLRSEIQNLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRLV 446

Query: 414 ISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473
           ISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA
Sbjct: 447 ISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 506

Query: 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSM 533
           RTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S+
Sbjct: 507 RTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 566

Query: 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEM 593
           E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI M
Sbjct: 567 ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGM 626

Query: 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           ++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|335033368|ref|ZP_08526736.1| RNA polymerase sigma factor [Agrobacterium sp. ATCC 31749]
 gi|333795306|gb|EGL66635.1| RNA polymerase sigma factor [Agrobacterium sp. ATCC 31749]
          Length = 684

 Score =  498 bits (1281), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 291/656 (44%), Positives = 396/656 (60%), Gaps = 63/656 (9%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IK  K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E    S
Sbjct: 31   VKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINVIEDE-DAEEAAPS 89

Query: 893  NITSDDDVEEA----------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 942
               SD D EE+          T  A +       RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 90   EDDSDSDNEESEGGELAPSGGTALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIA 149

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------GLIDKN 993
            IAKRIE G + MI  +   P T   ++I  D++++    + EI+D               
Sbjct: 150  IAKRIEAGRETMISGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQ 209

Query: 994  FSSNNRVIKGNKNNNEEK---------------------------ILIESSSADLSTEQL 1026
            F S  + I+ ++   EEK                              +   ++LS   +
Sbjct: 210  FQSPEK-IEADRKAAEEKEKTRRLRAPTGDEDVTDVGGDGLPPEEEEEDDDESNLSLAAM 268

Query: 1027 E-KLKYESLIKFSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML---- 1073
            E +L+ + +     I+  + K+RK  +++        G  S    + +  + ++++    
Sbjct: 269  EAELRPQVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVK 328

Query: 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 1133
             +      I+ L + L +   ++ Q E ++L +     G+ R  F++ +   E++ NW+ 
Sbjct: 329  SLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLA-ESYGVKRDSFLEQYHGAELDPNWMK 387

Query: 1134 NETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 1192
            + T +    +         +I+E++Q++ NL T+  + + + R I   +  GE +AR AK
Sbjct: 388  SITNLAARGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAK 447

Query: 1193 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252
            +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 448  KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 507

Query: 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 1312
            QAITRSIADQARTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK
Sbjct: 508  QAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRK 567

Query: 1313 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 1372
            ++KIAKEP+S+E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE 
Sbjct: 568  VLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREE 627

Query: 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 628  RVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 683



 Score =  480 bits (1236), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 283/643 (44%), Positives = 386/643 (60%), Gaps = 63/643 (9%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IK  K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E    S
Sbjct: 31  VKKMIKAAKKRGYVTMDELNSVLPSEEVTSEQIEDTMAMLSDMGINVIEDE-DAEEAAPS 89

Query: 103 NITSDDDVEEA----------TEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIE 152
              SD D EE+          T  A +       RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 90  EDDSDSDNEESEGGELAPSGGTALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIA 149

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD---------GLIDKN 203
           IAKRIE G + MI  +   P T   ++I  D++++    + EI+D               
Sbjct: 150 IAKRIEAGRETMISGLCESPLTFQALIIWRDELNEGTTLLREIIDLETTYSGPEAKAAPQ 209

Query: 204 FSSNNRVIKGNKNNNEEK---------------------------ILIESSSADLSTEQL 236
           F S  + I+ ++   EEK                              +   ++LS   +
Sbjct: 210 FQSPEK-IEADRKAAEEKEKTRRLRAPTGDEDVTDVGGDGLPPEEEEEDDDESNLSLAAM 268

Query: 237 E-KLKYESLIKFSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML---- 283
           E +L+ + +     I+  + K+RK  +++        G  S    + +  + ++++    
Sbjct: 269 EAELRPQVMETLDTIADTYKKLRKLQDQQVEARLACTGTLSSGQERRYKELKDQLITAVK 328

Query: 284 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVD 343
            +      I+ L + L +   ++ Q E ++L +     G+ R  F++ +   E++ NW+ 
Sbjct: 329 SLSLNQNRIDSLVEQLYDISKRLMQNEGRLLRLA-ESYGVKRDSFLEQYHGAELDPNWMK 387

Query: 344 NETKIQ-HDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAK 402
           + T +    +         +I+E++Q++ NL T+  + + + R I   +  GE +AR AK
Sbjct: 388 SITNLAARGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARIAK 447

Query: 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462
           +EM EANLRLVISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR
Sbjct: 448 KEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 507

Query: 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 522
           QAITRSIADQARTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK
Sbjct: 508 QAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRK 567

Query: 523 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRES 582
           ++KIAKEP+S+E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE 
Sbjct: 568 VLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREE 627

Query: 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           +VLRMRFGI M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 628 RVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|444310477|ref|ZP_21146098.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium M86]
 gi|443486039|gb|ELT48820.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium M86]
          Length = 673

 Score =  498 bits (1281), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 290/646 (44%), Positives = 397/646 (61%), Gaps = 54/646 (8%)

Query: 833  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 892
             K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31   VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 893  NITSDDDVEEATEAALSTVDSDF----------GRTKDPIKMYMREMGSVELLTRDGEIE 942
               SDDD EE  E  + +  +             RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 88   EDNSDDDSEEGGERLVESGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIA 147

Query: 943  IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-------------GL 989
            IAKRIE G + MI  +   P T   I+I  D+++ + I + EI+D              +
Sbjct: 148  IAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNILLREIIDLETTYAGPEAKQAPV 207

Query: 990  IDKNFSSNNRVIKGNKNNNEEKILIESSS-------------ADLSTEQLE-KLKYESLI 1035
            I++      R  K  + + ++  +                  A+LS   +E +L+ + + 
Sbjct: 208  IERVEEEKPRDDKPQRRSRDDDDITNVGGDMPVEEEEEDEDEANLSLAAMEAELRPQVME 267

Query: 1036 KFSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIE 1083
                I+  + K+RK  +++        G  S S  + +  + ++++     +      IE
Sbjct: 268  TLDLIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIE 327

Query: 1084 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDY 1142
            +L + L +   ++ Q E ++L +     G+ R  F+K +  +E++  WV+  + +    +
Sbjct: 328  QLVEQLYDINKRLVQNEGKLLRLA-ESFGVRREEFLKEYQGHELDPKWVERVSTLSARGW 386

Query: 1143 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 1202
                 +   +I  L+ ++  L T+  + + + R I  ++  GE +A  AK+EM EANLRL
Sbjct: 387  KEFAAKEERTIDRLRSEIQMLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRL 446

Query: 1203 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262
            VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 447  VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 506

Query: 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 1322
            ARTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S
Sbjct: 507  ARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS 566

Query: 1323 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 1382
            +E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI 
Sbjct: 567  LETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIG 626

Query: 1383 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428
            M++DHTLEEVG+QF VTRERIRQIEAKALRKL+HPSR  KL+ FL+
Sbjct: 627  MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 672



 Score =  480 bits (1236), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 282/633 (44%), Positives = 387/633 (61%), Gaps = 54/633 (8%)

Query: 43  FKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLS 102
            K +IKL K+RGY+T  E+N  LP + +  E IE  +     M I+V E   D E     
Sbjct: 31  VKKMIKLAKKRGYVTMDELNAVLPSEEVTSEQIEDTMSMLSDMGINVVE---DDEQDNDR 87

Query: 103 NITSDDDVEEATEAALSTVDSDF----------GRTKDPIKMYMREMGSVELLTRDGEIE 152
              SDDD EE  E  + +  +             RT DP++MY+REMGSVELL+R+GEI 
Sbjct: 88  EDNSDDDSEEGGERLVESGGTAVATTTTKKEPTDRTDDPVRMYLREMGSVELLSREGEIA 147

Query: 153 IAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVD-------------GL 199
           IAKRIE G + MI  +   P T   I+I  D+++ + I + EI+D              +
Sbjct: 148 IAKRIEAGRETMIAGLCESPLTFQAIIIWRDQLNDSNILLREIIDLETTYAGPEAKQAPV 207

Query: 200 IDKNFSSNNRVIKGNKNNNEEKILIESSS-------------ADLSTEQLE-KLKYESLI 245
           I++      R  K  + + ++  +                  A+LS   +E +L+ + + 
Sbjct: 208 IERVEEEKPRDDKPQRRSRDDDDITNVGGDMPVEEEEEDEDEANLSLAAMEAELRPQVME 267

Query: 246 KFSNISFHFDKMRKAFEKE--------GYNSESYIKAHNNISNEML----GIRFTAKSIE 293
               I+  + K+RK  +++        G  S S  + +  + ++++     +      IE
Sbjct: 268 TLDLIADTYKKLRKLQDQQVEGRLAATGELSSSQERRYKELKDQLIKAVKSLSLNQNRIE 327

Query: 294 KLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQ-HDY 352
           +L + L +   ++ Q E ++L +     G+ R  F+K +  +E++  WV+  + +    +
Sbjct: 328 QLVEQLYDINKRLVQNEGKLLRLA-ESFGVRREEFLKEYQGHELDPKWVERVSTLSARGW 386

Query: 353 NLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRL 412
                +   +I  L+ ++  L T+  + + + R I  ++  GE +A  AK+EM EANLRL
Sbjct: 387 KEFAAKEERTIDRLRSEIQMLATETAISIGEFRRIVNQVQKGEREATIAKKEMVEANLRL 446

Query: 413 VISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472
           VISIAKKYT+RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ
Sbjct: 447 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 506

Query: 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVS 532
           ARTIRIPVHMIETINKI R SRQ+L E G EP P  +A K+ MP EK+RK++KIAKEP+S
Sbjct: 507 ARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS 566

Query: 533 MESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIE 592
           +E+PVGD+EDSHLGDFIED+N L P DAA+ A++R     +L SLTPRE +VLRMRFGI 
Sbjct: 567 LETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIG 626

Query: 593 MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625
           M++DHTLEEVG+QF VTRERIRQIEAKALRKL+
Sbjct: 627 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 659


  Database: nr
    Posted date:  Mar 3, 2013 10:45 PM
  Number of letters in database: 999,999,864
  Number of sequences in database:  2,912,245
  
  Database: /local_scratch/syshi//blastdatabase/nr.01
    Posted date:  Mar 3, 2013 10:52 PM
  Number of letters in database: 999,999,666
  Number of sequences in database:  2,912,720
  
  Database: /local_scratch/syshi//blastdatabase/nr.02
    Posted date:  Mar 3, 2013 10:58 PM
  Number of letters in database: 999,999,938
  Number of sequences in database:  3,014,250
  
  Database: /local_scratch/syshi//blastdatabase/nr.03
    Posted date:  Mar 3, 2013 11:03 PM
  Number of letters in database: 999,999,780
  Number of sequences in database:  2,805,020
  
  Database: /local_scratch/syshi//blastdatabase/nr.04
    Posted date:  Mar 3, 2013 11:08 PM
  Number of letters in database: 999,999,551
  Number of sequences in database:  2,816,253
  
  Database: /local_scratch/syshi//blastdatabase/nr.05
    Posted date:  Mar 3, 2013 11:13 PM
  Number of letters in database: 999,999,897
  Number of sequences in database:  2,981,387
  
  Database: /local_scratch/syshi//blastdatabase/nr.06
    Posted date:  Mar 3, 2013 11:18 PM
  Number of letters in database: 999,999,649
  Number of sequences in database:  2,911,476
  
  Database: /local_scratch/syshi//blastdatabase/nr.07
    Posted date:  Mar 3, 2013 11:24 PM
  Number of letters in database: 999,999,452
  Number of sequences in database:  2,920,260
  
  Database: /local_scratch/syshi//blastdatabase/nr.08
    Posted date:  Mar 3, 2013 11:25 PM
  Number of letters in database: 64,230,274
  Number of sequences in database:  189,558
  
Lambda     K      H
   0.318    0.135    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,476,623,785
Number of Sequences: 23463169
Number of extensions: 866391787
Number of successful extensions: 3242380
Number of sequences better than 100.0: 1000
Number of HSP's better than 100.0 without gapping: 15300
Number of HSP's successfully gapped in prelim test: 4007
Number of HSP's that attempted gapping in prelim test: 3162670
Number of HSP's gapped (non-prelim): 53342
length of query: 1432
length of database: 8,064,228,071
effective HSP length: 156
effective length of query: 1276
effective length of database: 8,698,941,003
effective search space: 11099848719828
effective search space used: 11099848719828
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 84 (37.0 bits)